I recorded some scenes this weekend with a Lav in my XLR channel 1 input, and boom in XLR channel 2. How would I go about capturing the footage with CS 3 will keeping channel 1 and 2 separate but both recorded in with the clips?

Just capture it normally. When you've decided whether L or R is better, us the audio effect to Fill Left or Fill Right, depending on which you prefer.

what do you mean? I don`t have CS 3 yet, I`m trying to decide if I should buy it. Does it put channel 1 and 2 on separate tracks?

Premiere Pro CS3 will allow you to select a stereo clip and break it out to two mono clips and they will still be linked when you bring the video to the sequence.

Clip > Audio Options > Source Channel Mappings