I fill my T5 by using an appropriately sized clear plastic tube, inserting one into the tranny and routing the other up into the engine bay, where an assistant pours the fluid into a funnel into the tube, and I stay under the car to make sure all is well.
I could do it on my own, 'cause the tube sticks in far enough to hold in place, and I just keep funneling the fluid in until it's near capacity, and then I watch for it to come back out of the fill hole, indicating that the unit it full.
I can relate to the poster's error - I had a brand new 1993 Chev Cavalier with a manual trans, and the first time I went to change the fluid I ended up removing the completely wrong "bolt" which looked like a good candidate for a drain plug to me at the time. I got lucky - bolt went back in and my dad is still driving that same car with the original tranny in it today with almost 150,000 miles on it. I was 19 and "winging it". I'll never do that again.