An automatic transmission has a pump. It is usually located inside the casing, right behind the torque converter. You don't have access to it from the outside. It only pumps when the engine is running. It draws fluid from the pan on the bottom of the transmission casing, sends it to the cooler in the radiator and then to the bands in the transmission via the valve body. Pressure on the various bands force their respective clutch packs to engage, which effectively "engages" the various gears.
So, when you pull a trans cooling with engine off, you SHOULD get a LITTLE fluid - there is usually a check valve in the valve body that prevents all the fluid from running back to the pan when the engine is off. The cooler in the radiator is a little higher the the cooling lines so gravity will push some out. If none comes out, don't freak out. The check valve ( basically a little metal ball in the trans valve body with a spring behind it) might be just getting a little "lazy" after all these years and has allowed all the fluid to run back into the pan. Don't freak but it is something to note.
Check the fluid level on the trans dip stick. I have a manual trans in mine so I don't recall the specifics for a Cherokee but generally this should be done engine running and up to operating temperature (fluids expand when they get warm - check it cold it will show low). Since you are finishing a rebuild, I'd just check to see that there is fluid on the dipstick. Maybe put a half pint in just to cover what probably got lost somewhere along the way, and the continue initial startup. Check again once the motor is warmed up and before you drive somewhere.