Matt, there should be a command key on both sides of the keyboard for helping to reduce any muscle strain. For the command key on the left, I always use my left thumb.

Windows shortcut keys are quite barbaric and nonexistent when compared to what you have available in Mac OS X. In the OS, shortcuts should generally always be command-key based unless they are extended shortcuts which would then employ an additional modifier. So unless you're switching to a different OS (VM, etc.) you'll be pretty much using only the single modifier. CTRL is rarely used as a shortcut modifier, and then typically in combination with command. CTRL on the Mac is used for its original purpose, for sending control sequences to terminal sessions.