If you are putting the two drives in RAID0 then you will need to do the alignment only once as the two drives will effectively be treated as a single volume, the alignment makes sure that the drives are set to the same starting block - and hence the stripe is set correctly (as I understand it).
For mine, I entered the Intel Matrix Storage Mgr (Ctrl + I at POST) to set the drives into a RAID0 array with a 128k stripe size (apparently this is best for Vista), then booted from the Vista disk and went to the recovery console and then followed the full details and instructions
here on the OCZ Forums. There are several methods of doing it - as I said I did it from the Vista Recovery Disk method as shown in post#3 on that page (although with this method you will need a disk with the RAID driver available to you, on USB perhaps?) I'm pretty sure the recommended partition alignment for RAID0 on the Vertex's is 128.
Once aligned you can then go ahead and install your OS. Then you'll need to get the tweaks done for SSD performance (
link here) and then I recommend you get Windows and drivers updated and finally DO AN IMAGE! (use something like Acronis True Image)
Occasionally there may be new firmware released for the drives and there are guides on flashing (old method
here, and new method
here) - this will completely clear the drive tho - so the image you've done can then be used to quickly restore the array. (I have a pair of Sammy F1's in RAID1 where my image is stored for easy access - boot from recovery disk, point to image, sit back and have coffee!)
And basically that's all there is to it! Easy!

Hope this helps.