Would a senator or equestrian have "run" the military, with the Emperor as Commander in Chief, or was each legion law unto it's own?
No. During the Republic that consuls acted as commanders-in-chief, but this was an "on the spot" position--if they were physically present at the army they were automatically in charge, but given the difficulties of communication actually micromanaging from a distance was practically impossible. If more soldiers needed to be committed to a particular theater, it would usually be the job of the consul to raise the troops, or a departing consul who is taking up the post of governor in the province. However, the Senate could also raise troops and send them over without a change in command.
The Principate operated in much the same way, except that the emperor operated on top of the system.