There's two ways I fill it depending on which car I'm working on. In my 90 GT, I simply take out the fill plug, take off the shifter, and pour in a quart at a time through the shifter opening, and stop occasionally during that third quart to keep an eye on the fill hole. When I'm done I just put the shifter back on, and insert the fill plug into it's proper place.
On my 68 coupe (with a T5 swap), the hole in the trans tunnel is not big enough for me to pull the shifter (yes, if I want to change the shifter or pull it, I have to pull the trans). In this case I use a siphon pump that you can get from Autozone for like 12$. I put one hose into the trans fluid, and the other hose into the trans where the fill plug is. Then all I have to do is pump the fluid in (it has a hand pump). I actually almost prefer this method, and sometimes use it on my 90. There's less potential for a mess.