When we wanted to start the subject in a previously recorded state, we'd pull out the corresponding vellum and lay it in a appropriate spot in the capture area. We had a piece of blackened cardboard, from the middle of which we'd cut an oversized foot shape. We'd slide the cardboard under the vellum and mark the feet onto the floor. For Nintendo's Major League Baseball with Ken Griffey Jr. developer Angel Studios used vellum to mark the foot positions of motion-captured actors. Name your files something short but meaningful.
Directory structures are also very important to working efficiently.
Experiment to find what works for you. The first is that your final motions, taken as a whole, should display as wide a range of detail as you can manage. If you put control first, you may not be able to include things like special turning moves. What you gain by this is that the player has precise control of the character at every moment. What you lose is the chance to include interesting, character-defining motions.