Side Moldings?
 

I have read the different posts and i knew that I can fill the trench with bondo, but then I was told that it would crack because of the great amount of bondo. is this true and if it is what could I use to fill it? What do they use at body shops?

Yep, it's true...you asked that here.
The pros will put a piece of metal in there, weld it and bondo over that to smooth it down.

Bondo's wonderful in small amounts...but....nah..get it done right..so you don't regret it.

buddy of mine bought a hatch with the moldings bondo'd... it cracked eventually in places but for the most part held up. but it wasn't a pure bondo mix, it was something else. regardless he ended up chipping all that shit out and now is going with JDM thin side moldings.

pro - weld sheet metal and bondo the weld

crap - ass load of bondo