I drained the transmission pan and reinstalled the plug then added more fluid through the opening for the dipstick. I found posts saying there's a fill hole on the transmission pan and posts saying just pour it in the dipstick opening. Did I fill incorrectly? I've already driven around a bit today. Should I be concerned?

You're fine. Fluid ends up in the same place. I believe the automatic is through the dip stick and manual has an opening similar to the differential.

Whenever i have added fluid to my 99, it has always been through the dipstick.

Filling it through the dip stick is how I did it in my 1998.