It's normal for the fluid to back up into the master until all of the air is out. You are compressing the air somewhere in the system and that's what's pushing the fluid back. I keep going around the truck several times to get the air out. There's no real good was to get the air out when the master is as low as the bleeders (can't gravity bleed). Also, make sure the pedal rod is adjusted properly or you may never feel a good pedal,
Scott