To answer some of your questions directly:
■Any graphics card with the same interface as the motherboard will work (in your case, PCI-e x16).
■Nvidia Quadro cards have dual link DVI. This allows you to run two monitors from what seems to be one DVI port (through an included Y adapter). Also, most modern graphics cards have two outputs (of varying types); 'performance' cards tend to have dual DVI ports.
RAID:
RAID is the use of several identical discs in an array to give better performance, and/or better data integrity. There are a number of RAID 'modes' that have different uses/benefits, but the one you've probably got wind of is RAID 0 - "striping". In a RAID 0 array, two or more discs (of identical capacity) operate as one 'physical drive' that appears (to operating systems) as a volume the sum total size of all the drives in the array (ie three 500GB drives in RAID 0 show as one 1500GB volume). Imagine you have a RAID 0 array with four drives. In layman's terms, if you save the word GOAT to the RAID volume, the word is divided into four pieces and one letter will be written on each disk at the same moment (drive 1 writes "G", drive 2 writes "O", etc). This is effectively four times faster than writing each letter of GOAT to a single drive, as in the time one drive would be finished writing "G", the RAID array would write the entire word. This works in the same way when reading files - each disk in the RAID array will read its letter simultaneously and the whole word will be loaded in the time a single drive would have read one letter. The more disks are in an array, the faster files can be written and read (by a factor of how many disks there are), BUT with every disk you [strike]add[/strike] have in a RAID 0 array, the chance of failure also increases. EDIT: Note that once a RAID array is created, drives cannot be added.
Due to the nature of a RAID 0 array, if one drive is taken away, all data is corrupted. This is because (in our four drive scenario) one forth of every file will be missing. Considering catastrophic drive failure, with four drives, you are four times more likely to have a drive failure than you are with one drive. A 1TB RAID 0 volume made of four drives is thus four times more likely to fail than a single physical 1TB drive. This actually happened to my brother a few years ago - he had 5x 200GB drives in a RAID 0 array, one drive died, and he lost every bit of that 1TB. In short, the factor of speed increase in a RAID 0 array matches that of the chance of failure.
With exception to RAID 0, the primary purpose of all RAID modes is data integrity. At Weta Digital (in New Zealand), a RAID mode is used (can't remember what number) that has 3 drives in RAID 0 and one spare (redundant). When any one of the RAID 0 drives shows signs of failing, all its data is copied to the spare drive, and a technician is alerted to replace the faulty drive (all automatically).
I don't recommend using RAID for file storage unless you have a good reason to (ie. dealing with files bigger than any one drive can handle). I do however recommend having a RAID 0 of Solid State Drives to run your operating system and programs from (but not to use as a scratch disk). I have one SSD for OS and main applications and it is blazing fast - 2,3 or 4 of them in RAID 0 would be incredible. I'll note here that one big RAID volume really wouldn't suit your needs as outlined below.
Drives for paging, source footage, etc:
■Premier allows you to set scratch disks (for various types of temporary files) when creating a project. Generally this is where previews are rendered (when you press enter).
■If you have enough RAM, the operating systems page file probably won't get used, and it's best to avoid using it anyway (but for reference, the page file settings are accessible by right clicking on my computer -> properties -> clicking advanced system settings on the left [vista/win7] -> click "settings" button under performance heading -> Advanced tab -> Change button...and don't forget to click set when you change a drives settings).
■For optimal performance, footage should be on an independent drive. In fact, for optimal performance, software, footage, and scratch should all be on different physical discs. In my system I have a physical drive for OS, a physical drive with documents/photos/music on one partition and non-important programs on another, 3 physical drives for file storage, and one physical drive for scratch/current projects (they are archived to another drive when complete).
Hardware components:
As you've said you will be using a lot of After Effects, RAM is key to productivity. 12GB is good, but get more (or plan to at least) if you can. I have 9GB and AE chews through that no problem. Note I said productivity though - more RAM will just allow you to render more frames to RAM before it starts over-writing the older frames. Intel i7 is a must for this kind of machine, and it wouldn't hurt to overclock a little as they do so easily (I have a super-stable OC at 3.8GHz [on stock voltage] which gives me a 30% hard speed increase over stock). For a graphics card, memory [again] is important, although you don't want to skimp on power. More graphics power will result in smoother use of CS4 and CS5 apps. Editing a single 8MP image in Photoshop uses about 300MB of VRAM on average for me and I see the GPU usage sky rocket when doing any simple editing/manipulating tasks.
For upgradability I would suggest an LGA 1366 i7 as this will future-proof you a little for CPUs. As far as other components are concerned, you are only limited by the number of PCI slots, SATA headers, and other headers on the motherboard. The type of most interfaces used on today's motherboards are unlikely to change in any significant period of time (as in, when they do, you computer will be old news).
If you want to sacrifice performance for price, your safest bets are to get an el-cheapo graphics card and keyboard/mouse, and don't get the bluray drive yet (they are really expensive and I doubt it would get used much initially). You'd be okay to get cheaper CPU, RAM and monitors for now, but in my experience that'll just end up being more expensive in the long run. The parts you should absolutely not compromise on are (primarily) motherboard and (secondly) power supply. Instead of getting cheaper RAM, the obvious thing would be to get less (good quality) RAM to start with and then add more sticks as you get more money (buying packs of RAM though, not single sticks).
One last note which I'm sure you are already aware of - you will need to run the 64bit version of Windows 7 to use more than 4GB of RAM.
Hope this all helps,
Stecman