Fill it until it just starts to come out of the filler hole.
**CORRECTION**
Sorry, for some reason I thought you meant the differential.
I believe it takes 3.5-3.8 quarts.
Might be a good idea to pick up one of those Haynes Mustang Manuals or something similiar. All specs and fluid capacities are detailed and very helpful.
That bullet archive link is a good place to get familiar with it. Also, everyone should have a Haynes manual. They have all the info you need for routine maint.
You can fill the tranny by taking off the shifter which is what I do. The shifter can be a bitch to remove sometimes. Just make sure you use RTV or if you use a shifter gasket make sure its in good shape before you reinstall the shifter.
I've tried the filler plug but it gets messy sometimes and space is very limited if you're working on your back.