Felt seal at window frame/body fitment

[RogueEngineer]

I recently got around to installing a new set of the felt flaps that run along the body where the window frame compresses the door seal. The fitment isn't great (the screw holes closest to the hood don't align) and I have to really slam my doors to get them to shut.

Should I have installed these prior to the door seals? It almost seems like they are meant to 'cup' the door seal bulb.

Any pro tips for these?