Help understanding boot drives/storage drives

First – SSD speed is due to the Very low access time general < a couple of millisecond vs a typical 7200 RPM HDD with a access time around 12 -> 12.6 millisecond. HDD most move head and platter mechanically to where the data is while an SSD does NOT. The biggest effect is on small file (4K Random) data retrieval which is the most important parameter for an OS + Program drive, SSD typically 40 x 100 times faster.
2nd An SSD will ONLY speed up the read/writes to the SSD.
.. This means that boot time and program load times are greatly reduced compare to reading and writing to a Slow mechanical HDD. Typical OS load time (boot, but excludes post); for win 7 around 15->20 sec, for Windows 8 My laptop from time I press Power on to displaying a web page is 8 SECOND.
.. An SSD will NOT make a program Run faster (only Load faster), Web surfing is not effected as you are at the mercy of your provider. No increase in FPS for games – Game will load faster and Maps will load faster – providing they are on the SSD and Not on the HDD.
3rd: I’m finding that SSDs are more reliable than Consumer grade HDDs

More to come – selection of SSD and HDDs

Boot vs storage

First off, don't get hung up and SSD vs HDD. Windows sees an SSD as (mostly) just a regular hard drive. They're just really, really fast. No moving parts.

Splitting things into multiple drives serves several purposes. Putting the OS and some applications on one drive, and all of your 'stuff' (movies, music, etc) prevents a major hassle when you might have to reinstall the OS. Your 'stuff' is untouched over there on the other drive, and won't get wiped out during the OS reinstall.

Putting the OS on an SSD really speeds up operations, and gives the whole PC a new feel. But because the SSD is so comparatively expensive, unless you have really deep pockets we can't use it for everything. 4TB of SSD space would be around $4,000.
So we put things that don't need that speed boost on a spinning drive. Music, for instance. In my house, the music lives on a whole different PC in another room. Shared folder, mapped to a drive letter, accessible through the network.

Installing your most used applications on the SSD also gives a new feel to the PC. MS Office and some of the files I use live on an SSD. Opening a moderately complex Excel file is near instantaneous. It's open almost before my finger stops moving from the click.

As far as the installation on only that drive...when you install, disconnect any other drives. Windows will put everything it needs on the one connected drive, be it an SSD or HDD.
Then connect all the other drives and off you go.

Installation of applications:
With a 128gb drive, you can probably put most of your applications on it. But some things don't really benefit from being on the SSD vs on an HDD. Gameplay for instance. Yes, the game opens a little faster, but there is no difference in actual gameplay once it is open. And some games are HUGE. So my Steam folder lives on a spinning drive.
Same with movies. When watching a movie, there is no benefit from having it live on the SSD. The movie player can get it just fine from a spinning disk.

For your new build, I'd suggest instead of a single, large, 4TB drive, get 4 x 1TB drives. If the single 4TB drive dies, you've lost everything. If a single 1TB drive dies, the other 3 are just fine.

Part 2
SSD selection:
1) DO NOT use performance as your sole selection criteria. I have a 256 gig Crucial M4 (old drive BUT very reliable/low user problems), a 256 gig Samsung 830 and a 256 Gig Samsung 840 Pro (replaces the 830). Using AS SSD benchmark the M4 and the 830 both have an overall score of mid 700s while the 840 Pro scores a WHOOPING 1100 – Big Increase, BUT does NOT translate into any significant performance increase in real life day-2-day Performance difference. You would be Hard pressed to tell which of my systems have which SSD as an OS + program drive.
My Recommended list:
A) Crucial M4, Plextor M5P, Samsung 830 (if you can still find it). Have an excellent track record for Reliability (been out for several years) and Low User Problems). Best cost/performance drives.
B) If you want the absolute best, then the Samsung 840 Pro. Higher cost, But My choice for a laptop as it Has about the best LOW power consumption.
C) Finally, my budget pick is the Samsung 840 Non-Pro. Uses TLC NAND, which has a lower Max write cycles vs MLC and Toggle NAND
2) Size: Generally for Most the 128 gig is optimum recommended size. If Have the Money to splurge then I recommend either a larger 256 Gig SS, or a 128 gig OS + Program with a 256 gig “working/Overflow” drive. All my systems have two SSDs + HDD(s). On the 2nd SSD I store all my (A) most often accessed data, and (B) Currently working on files – Once I complete working on them (ie video and photos) I then move them to the HDD. Comment on size: EX a 128 gig SSD, the max available space is approx. 97 Gigs, Much lower than the advertised 128 Gigs. First you lose about 7 gigs when formatting – same as a HDD. 2nd with SSDs you need to leave 20 % Free (unused), this is so Wear Leaving, Garbage Collector, and TRIM can work their magic to maintain the performance level to manufs spec – Failure to do this can result in an SSD NOT performing much better than a HDD!

HDD selection:
Currently the ONLY two Consumer HDDs that I recommend are the WD Black and the Samsung F3 (Bought by Seagate, But still manuf at same plant, by same people). Enterprise drives are Fine but cost considerably more. Just check the stats at Newegg for the WD “Green” 3 TB drives – The “blue drives are not much better. Another indication is that WD only warrants the Green 3 TB drive for 2 Years, the Black has a 5 year warranty – Wonder Why – LOLs.
Myself, I limit my max size for Consumer grade HDDs to 1 TB. 1 TB drives seams more reliable (less failures) than drives that are > 1TB. (Only factor here is availability of Slots in case). Only Lose 1 TB of data vs 3 TBs of files when (IF) it fails. Plus it simplifies my back up.

Part 3 - OS Installation coming.

Part 3
Installing OS:
Really NO different than installing Win 7 on a Modern HDD on a Modern MB.
1) Disconnect ALL other HDs (2nd SSD and all Storage HDD). This is to PREVENT OS from installing the “small” system partition on a 2nd drive. If 2nd drive fails you cannot boot to OS on first drive. “Same” rule in just using two HDDs
2) When first booting to Windows Install, go to BIOS and Verify/change Control to AHCI (Sata) can be used if planning on raiding any drives – just not recommended. This is the same for newer HDDs that allow advanced error detection, For SSDs it is require to allow the TRIM command to be passed plus advance error detection.
3) Once Windows install has been completed, Windows updates installed, drivers installed, and programs installed, THEN:
… Disable Hibernation. Three reasons: (1) Saves a space equal to ram on SSD (8 gigs saved on a System with 8 gigs of ram. (2) In the past, waking from “sleep” has caused problems with SSDs, pretty much resolved. (3) Hibernation really not need as Boot time is so much faster than a HDD.
http://support.microsoft.com/kb/920730
.. Manage Your page File (Virtual Memory). HDD and SSDs. For a => 8 gig Ram system, set BOTH min and MAX to the SAME value, recommend setting both to 1024 mbs. For SSDs, windows typically use up to 1.5 x Ram (12 gigs) for space and dynamic changes the size. For SSDs This saves about 11 Gigs of space PLUS reduces writes. I also do this for HDDs with OS, but for a different reason, It reduces fragmentation.
http://windows.microsoft.com/en-us/windows-vista/change-the-size-of-virtual-memory
.. Last, Manage the space allowed for restore points. Each restore point takes 300 mbs, just twenty Restore point = 6 Gigs. This folder can get huge if allowed, For HDD with TBs of space not a problem. Myself I just disable and rely on below system image to restore my SSD.
http://www.howtogeek.com/howto/3187/disable-system-restore-in-windows-7/

Last Recommendation (also valid for HDDs) – USE windows Back-up app to create a system image of your OS drive (partition). Go to Control panel, System, and then back up. On left side select system image. Windows will select a 2nd drive (HDD) for storing this image. NOTE I also back up this image to an external HDD. When Done windows will prompt you to create a bootable System restore disk (Can be omitted and use the windows Installation disk).

If you ever need to re-install windows – NO re-install, No wait for windows Updates, NO reload drivers, and NO re-install programs. Insert Repair disk, or installation disk, Select Repair, then restore using image file. 15 Minutes later Wham-bam-thank you ____ reboot to EXACTLY the way the system was when you created this back up image – Of course you will have to do any changes mad since image was created.

From "Part 2"
Currently the ONLY two Consumer HDDs that I recommend are the WD Black and the Samsung F3 (Bought by Seagate, But still manuf at same plant, by same people)