I have a couple questions with SLI. I have just bought another 8800GT to run in SLI mode. Unfortunately the clock speeds are a bit different. So, first question. If I am putting the higher clock speed in the primary slot is it getting underclocked by the slower one, or is it bring the slower one up to its clock speed? Second question.    Assuming my faster card is getting underclocked, can I overclocked the slower one to the same speed as the faster one? Also, if anyone knows how I should have this set up as far as which card in which slot feel free to unform me  

Originally to use SLI the video cards had to be identical – same GPU, same manufacturer and even same BIOS version. From GeForce driver release 80 on nVidia relaxed a little bit and now the video cards can be from different manufacturers, but they must be based on the same GPU. This rule is valid for all versions of SLI (SLI, Quad SLI and Three-way SLI).
 
http://www.hardwaresecrets.com/article/391/4

Put the more overclocked version in the top PCI-E slot. It will automatically overclock the lower one to the same speed.

Thats why I'm asking. I've heard two different things when using different clock speeds (but the same GPU). I was told that in order to find a median you should put the faster clocked card in the primary so that it will fall to the slower card's speed. Then I read the if the faster clock is in the primary PCIe slot that it actually raises the clock speed of the secoundary card. I'm getting a lot of graphic lag and I was thinking maybe its becuase the secondary (slower) card is unstable running at the higher speed.  
 
MSI NX8800GT 660Mhz/1900Mhz
PNY VCG88512GXPB 600Mhz/1800Mhz

Also I bought this board GA-M57SLI-S4 AM2, its says PCIe x16(2). But when I was looking under the nvidia control panel the primary is running at x16 and the secondary at x8. Is that normal?

Yep, same as mine.  
The 570SLi chipset, can only run x8 lanes for SLi, not full x16 lanes. Don't worry, I'm barely bottlenecked with my GTXs, so you won't have a problem with GTs
GPU-Z identifies one card as x16 and the other as x8, I guess it's just an anomaly.

Thanks for the help. I'm thinking that if my slower card is actually running the same as my OCed card then maybe I just need to get a better heatsink. Any programs you recomend to check clock speeds?

take a look into riva tuner. It can monitor and overclock your graphics cards. You should be able to run at least 700core, 1700shader and 1000mem with SLI

 
Check the temperatures and raise the fan speed with Rivatuner if necessary.

 
Actually the faster card will underclock itself to match the speed of the slower card.  

aha, see this is where I get confused. I've heard both stories. I was considering putting my OCed card in the secondary slot so that the slower one will actually increase its clock.

Okay, now I think I may have a problem. I installed Rivatuner and its showing one card running at 663/1900 and the other 601/1800. Now, regardless on whether ones being under or overclocked, they should both be the same correct?

Is it normal for Rivatuner not to let me overclock the second card? When I go to the overclocking window for the second card it won't let me move the sliders.

Please post screenshot as I don't get a second window, either for my current rig or on my previous set up which was with a pair of 7900GT's that had different clock speeds.

Actually I have no idea how to post a screenshot on here.  

Try using this http://www.evga.com/articles/405.asp Its brand new, has a great GUI, and is very functional, and easy to use

I use this site http://load.imageshack.us/, but there are others that may suit you better.

I think I figured out part of the problem. I noticed when I restarted my computer that the second card dropped to a core of 339Mhz. WoW! I took off my S3 power saving option in the bios and it is a constant now. Although the core clock for the secondary is still different than the primary it is running at 601Mhz. I used Rivatuner to set the clock speed and now they are both the same. I shouldn't have to rely on rivatuner to make the cores the same speed but it is working.

I see you are having the same problem I had, btw sorry I did not read all the posts before posting mine. I put the slower card in primary slot and both worked at lower speeds, then i tried to oc with riva tuner 2.06,2.07,2.08 and no matter what anyone says it's not sli friendly if you ask me so i oc'd with ntune to see how far can i go. After I was 100% sure it's stable ( furmark 10 minutes--atitool artifact scan 1 hour, 3dmark @1680 8AA 16AF 3 runs ), I flashed bios of both cards to same clock,shader and memory speeds.