Get out the silicone or drill a hole!
So let me get the right, you have fiberglass door inserts or metal doors?
You said soemthing about inserts which tells me fiberglass but then you talk about a metal door. If its the inserts then I used POR-15 seam sealer which works great. I sealed around the sides and bottom so water couldn't enter. The canvas doors do let some water in but thats to be expected.
For metal doors, you definately will need new seals at the window. This will not only keep most of the water out but will also stop the window rattle. If the door seals are tight to the door, look at the corners where the gaskets meet each other for a gap. If you do use silicone to fill in a gap you can add a thin coat of grease or petrollium jelly to the areas that you don't want it to stick to. Once the silicone is dry you can wipe off the grease and you got a silicone seal. Check the top to windshield gasket, those can leak water on the floor. If its water on the pass side, make sure its not the heater core!