I have a Sony HVR-A1U. Now, i have a sennheiser m66 for my mic. If it's the only mic i plan on using, should i put the channel as Ch1-Ch2 or just Ch1. What's the difference between the two. Thanks.

channel 1/2 will give you audio on both the LEFT and RIGHT channels.
channel 1 (only) will give you audio on the LEFT channel only leaving the RIGHT channel open for another audio source. If you're only using 1 mic I suggest you go to channel 1/2 and adjust the 2 channels to different levels so as to be able to control overmodulation better. This method will give you 2 channels in post so if there is some crashing (clipping) on channel 1 the with channel 2 set lower you should be OK.
HTHs
Don