Just continue until the story won't let you progress and talking to Maria will upgrade any rank quests (whether you have the first or the second). What you say is because it's set up the old way where the cap was 3 for all the girls, leveing the same one or two to the max can cause weird bugs sometimes. This is fixed in v0.8.0 and everything to do with proof of trust will change radically in v0.9.0.