The points do impact relationships and how far some scenes may go.
From what i remember they actually don't -- the only real use they have is a check at the very end whether the player can get the epilogue with the given girl(s). But they aren't used for anything in the game proper.
There is some scenes where the player has to pick "right" answers to continue on the girl's path, but these are unrelated to the relationship points, and don't check them.
I've been trying to balance everyone out but the whole thing with the help 'SHORTCAKE' (from the donut list) first or 2nd vs go to the church 1st vs 2nd threw me for a loop and then the Kiki or Ashely/Trisha as well....aaargh. Seems that even if you lose points you can make them back pretty soon after but I'm not sure if there are certain levels that affect if you can get further with a person (would like more interaction with Kiki but now low on points with her)
From personal experience, if you try to balance sister/Ashley points, especially with others, you can very well end up with not enough points to get either of their epilogues. Check the walkthrough for Ch.3 for details.
That said, Chapter 3 is pretty short and allows you to manually enter any amount of points you want instead of import. So the worst case scenario you can just enter high enough amounts there without having to replay the whole thing.