there's some rust in there and i want to get it out but the rubber thingy is in the way...

 

I very thin screwdriver.
Start to pry it up from the back.
Don't bend it to far because there is metal in it that can kink easy.

 

whats the purpose of those anyways? I ripped mine out because it trapped water underneath and caused the channel to rust

 

It is a rain gutter... just like on a house. Same purpose, takes water from one place and brings it to another.

 

This is how it's done on a hatch (the CRX may be a little different);

Use some pliers to grab the very end of the plastic (rubber) piece and pull it slightly rearward and upward. This will get it off the clip and metal pin that is under it.

Then gently pull the piece upward and out of the groove. The metal groove has a taper to it and that helps keep the piece in place.

There is another plastic clip and metal pin at the front.

As was said in one of the prior posts, the plastic piece has a metal piece molded in it and you should be careful to not bend it too much.

As for what it does; it's nothing more than a "cover" that hides the seam where the metal body panels are welded together. Even if you don't re-install it, there should be no problems with leaks. This assumes that the factory seam sealer is in good condition.

Wes