The shop manual has instructions on this, but mine is in pieces and I can't find the right piece so I'm working from memory.
I believe that you fill the pump up to the bottom of the hole and run it in one direction or the other and top off at regular intervals, which is key for not burning up the pump. After going all the way up and down many of the bubbles should be gone and a cycle or two should get it done. At least, that is my recollection.
Also, my AutoZone sells a cap with a long flexible tube that you can screw onto the ATF container. This or something like it is key for getting the fluid in without making a mess.