If you received the owner's manual, it should indicate what weight oils are required in each hole. Or get yourself a service manual for your model and year and check it for specs.
That's what I did when I did my first complete fluid change for all three holes. My '08 FLSTC requires 75W-140 for the tranny. I used Amsoil synthetic for the tranny; Mobil1 20W-50 in the engine and I did use H-D 20W-50 in the primary. If you follow and go "by the book", you cannot make a mistake IMHO.