So...... if your team is just littered with injuries.....so many that you can't activate a full 46.........when the game simulation starts, does it auto activate some players who are deactivated? If so, then what decides which ones it activates?

not sure, but in my one league each position on the OL has at least 1 injury

Yes, you are best off activating the least injured and/or the ones you are least concerned about exaggerating their injury. Bad things will happen if you enter a game sim below the minimum active players.

...yep and I'd suggest moving the injured players you do activate to the bottom of the depth chart which should lessen the chances they actually enter the game and aggravate the injury.

Just remember to move them back up the depth chart when they are healthy...don't leave your starting stud LB at the bottom of the depth chart for four games like I did once.