I just put a decent amount on my finger and dab it on...I understand what you are saying though. Sometimes it makes it easier once you have the aquaphor on your finger to put that finger on your tongue to wet it just a little bit. That makes it easier for me.
I put it on very gently and "dab" instead of rubbing across. If a bunch of stuff comes off by doing that, it probably wasn't meant to be on your lip anyway.