Step 1: Start Design on the CAD system
See Woodenbikes' genius "CAD" instructions to create a cardboard cutout of your body, so you can figure out proper positioning of wheels/seat/handlebars/etc. As he says...
"Using a sophisticated 2D CAD system (Cardboard Aided Design) life size cutout of your foot/leg thigh/back and arm, pivoting on brads at the joints, you can design the bike on the ground to explore sizing and clearance issues. My CAD system sometimes has a Gooey interface if I spill something on it while designing :-)
More seriously, like other CAD systems it has a GUI (Graspable User interface).
Make a cardboard cutout of your lower leg (with foot and pedal), thigh, torso, and straight arm (to a distance 2" back from your wrist). Use it to look for good riding position and clearances for knees to bars, heels to wheels etc. Use the CAD system to layout the riding position, cranks, wheels etc with attention for locating your hands, shoulder, seat-back angle, butt, knees and feet.
For detailed instruction on 12 Steps to designing a sweet handling recumbent, visit Bikesmith Design at http://bikesmithdesign.com/Design/12Steps.html