How can I change the command key to be the ctrl key for tmux. It's already mapped for other apps) tmux wants me to press Command+A (or Command+B by default, changed it by having set -g prefix C-a in my .tmux_conf file).

I have already switched Control and Command, so, in general, Control+C will now do Command+C, etc.

So how can I make tmux also use Control instead of Command ?
How did you switch control and command ? Did you use the "Modifier keys" tab from System Preferences > Keyboard ? By doing so, your keys will be switched on all the apps. I'm not sure this is exactly what you're looking for, if no please let me know.