I Have a 790i ultra with a E8400 with 4 sticks of 2gb Patriot 1800L series and a OCZ Z-SERIES 1000W 80+ Gold Certified 24PIN ATX 83A 12V Afc.
I have recently installed 2 Nvidia 550Ti's and ive noticed some lag when UAC pops up before I can run a game. There are lag spikes in less power consuming operations that dont make sense as well. What I want to know is if its wise to set my PCIe express up to say  handle the extra bandwidth of the cards. I have been reading that if you're messing around with the fsb you should keep your PCIe set to , so im just worried about pushing this Nvidia board too much and blowing it.
Don't change the PCI-E frequency, set it to 100 and leave it alone. You could damage your graphics cards by changing it to 133, max I've seen used is 103.
Just turn UAC off if it annoys you, the lag when doing every day things is more likely due to only having 2 cores, or an unstable overclock, I very much doubt its anything to do with your graphics cards.