I work on and build custom PCs for a living. I'm around other techs who do the same ( obviously ), my point is, "to each his own" with how you go about installing/building a new machine.
Biggest thing I can stress is always READ YOUR INSTRUCTIONS, EVEN IF THEY SUCK! I see techs get into trouble to often from getting ahead of themselves on a build. Most of the time you will need to mozy on over to the manufacturer's website for better documentation. Sometimes there is non at all, either with the product or on the website. If that happens, obviously google is or come to a site like this.
The air is dry right now. Anti-static precautions are really important during the colder months. If you have an Anti-Static wrist strap, use that. If not then every single time you go to touch your machine, touch a nearby piece of metal, ( doorknob, filing cabinet) then touch the casing or PSU, do this often. Even better, if you have a humidifier then get that puppy into the room and leave it to run with the door shut for a while. get to 65% or so of humidity.
Also handle your parts with care! Try not to touch the circuits ( I know its hard not to sometimes ) Always pick them up using the edges of the board.
Personally, whether I install the cpu before I put the MoBo in, just depends on if I'm in a hurry, and the type of case. If you bought an aftermarket CPU cooler, check your instructions! Most have an extra part that goes on the bottom of the MoBo.
Take your care and look it over good. Look for best places for routing cables ( if you care ). Install CD-roms and depending on how your HD housing is, your HDs as well.
Now, whip out your MoBo, Slap the cpu and ram on it. Careful with your CPU, be sure you are seated correctly as with certain sockets, I still cringe a little bit from the amount of force it can take to close the gate over the CPU. (Gate = metal housing with the lever). Leave your Graphics off till after mobo is in, that beast will get in your way. I suggest it be one of the last things.
Now, Drop in your MoBo, then drop in your PSU. And don't worry about the fan pointing down. (there should be a small amount of space between the bottom of the case and PSU bottom after you have the screws in tight, again depends on case.) Now, you have 2 options for the Fan on the bottom issue. For one, I own an Antec NineHundred. I bought a PSU with 2 fans on it so it pulls air from the front then out the back. So you can swap out your PSU. >OR< Take a dremel and cut yourself a grill ont he bottom of your case
~ As long as you don't have parts in it when u do it... you're gtg man. Be very sure that no metal filings hang around, short waiting to happen right there.
Now then, we have our CD/DVD in, Mobo w/ cpu & mem, and our PSU. Install your Hard Disk(s). Finally, your graphics card and any other addon cards ( be sure it goes in PCIe port 1).
Begin connecting data cables and do management as you see fit. ( a clean case, aka, not a rats nest of cables, will allow for better air flow, thus better cooling.) Then your power cables. You may have to use some force on the 20/24pin mobo power. Be CAREFULL, stick your finger under the edge of the mobo if when you insert that plug. You don't want to have your board flexing.
Go back over and check your work. If it looks good, power it up, go into your BIOS ( usually del key, splash screen will tell you ) and check to see that all your hardware is registering itself properly. If not you may need to either change a setting or two, OR, flash your BIOS (not as scary of a task as it used to be, and can be done with a USB flash drive). Main spec to check is your graphics cards settings in your BIOS. Most of the time you need to set the "Amount of RAM" correctly. So change that to whatever the amount is. Also check the other settings, use some common sense. Put your Windows disk in your drive, Save changes and reboot. Install windows. have fun!
On a lot of the builds I do, the customers want overclocking. Since most of the components you bought qualify as "Enthusiast" you can go have some fun in your BIOS overclocking. Most makers now have what I refer to as "Dummy Overclocking" were you will find a menu in the BIOS were you can just say, 5%, 10%, 15%, 20%.. and it will make the changes required for you. Most of the time 5% or 10% is stable ( no random crashes ) when you get up to 15% or more, Overclocking requires subtle voltage and timing changes. Unless you go read up on it, I don't advise ever changing a voltage setting, and if/when you do, you go by very small increments. You will find a lot of overclocking guides online, just realize not all components are the same, even if they are the same. Makes no sense right? you can have 2 cps from the same wafer, but one tests out faster than another, so its labeled faster and sold at a higher price. If you have noticed when reading reviews, people talking about "Unlocking" cores, especially on AMD cpus? That's my whole point. Those CPU's are actually higher grade, but just weren't quite able to qualify for the branding of said higher grade. So they disable the extra cores and sell it cheaper. There is no guarantee it will work every time.
I apologize, I believe I got wordy
If you need more help reply back. I'll check back periodically.