Put the keyboard between them. Even if you have the new programmable flight controllers, don't overly automate. You are going to have to reach around the cockpit in the real aircraft, so use the keyboard as the substitute for cockpit switches. Do automate viewing controls as much as possible.
Rudder pedals go on the floor, obviously.
The manual includes two chapters on Flight Training, Chapters 12 and 13. It's set up for practice in the Cessna 182. The 182 is bigger than most trainers, but its performance is closer to training aircraft than Flight Simulator 's other choices. This will make you move both the rudders and ailerons in unison to achieve smooth flight. Allowing the sim to do it automatically really doesn't prepare you for what's going to happen in the aircraft.