How can I change the shortcut keys for my MacBook Pro so it doesn't conflict with my remote Windows shortcuts?
You can disable some of the F-key shortcuts in System Preferences:
Just a suggestion: Look at the key mapping in windows and not the Mac side. remember that while Command is often control in windows, often times the option, fn, and control keys can be swapped.
Take a look at our application ShortStop which was made specifically for sending shortcuts through remote screen sessions.