Can I play games in a diff resolution than what my resolution is at when not playing games?

My resolution is 1152 x 864 and I was wondering would it be alright for me to play games with a different resolution, like 1280 x 960. I am constantly hitting the 'start' button to minimize my game and listen to music on YouTube, listen to podcasts, etc., will this mess with anything? I am using a GTX 460 graphics card, I don't know if this info is needed.