I drill the mortice draw bore holes before chopping the mortices. The next step is dry fitting the stretchers to the legs, making sure everything pulls up tight and square. I like to clamp once I'm happy with the dry fit.
I drilled the mortice holes with a brad point drill, using the same drill I insert it into the mortice draw bore holes and spin a little to make sure it is centered and then give her a whack to mark the center on the tenon. Next is disassembly of the legs and stretchers, using the marked centers as a reference move the center for the tenon draw bore hole slightly (about 1 to 2mm) toward the shoulder of the tenon. Drill the tenons, reassemble the legs and stretchers, making sure everything is square and pulled up tight and clamp it. I will use draw bore pins to help get everything alined and slightly round the tenon pin hole. Once every thing checks, pull one draw bore pin, replace it with a wood pin and drive the pin home. Repeat until every hole is filled :-).
The set up:
The tenon reference mark, make it big to see: