First off, the Mac "Command key" is not involved with "C-x". "C" is for "control". "Command" is often bound to the Emacs "Meta" key, which would be "M-x".

For C-x I generally hit Control with my left pinky and X with my left middle finger: since C-x is a "prefix" key, there's going to be another key I hit later and that will generally be hit with my left index finger.

However for the C-x C-s sequence I use my left index finger on X and my left middle finger for S. Same with C-x C-q.

For M-x I use my left thumb on the Meta key (my Mac's "Option" key in my case) and my left index finger on X.

Just like playing piano, there is no "right" way to map your fingers to the keys (everyone's hands are different, after all). If something feels wrong or is hurting, try using different fingers.