Wee!!! I'm all set up and it's very cool

I think I need to do some tweaking someone 'cause I am having a few issues, anything sound familiar?
When I boot up my computer the resolution of the main (#1) screen will not be the same as when I turned off the computer. Also on the main screen I can not seem to get a good resolution choice. I had it at 1280x1040 before I added the second monitor and when I put it at that resolution now it looks stretched (square images on screen are not perfectly square) and also the fonts look chunky.
Anything glaringly easy I need to check?