I am wanting to start making some molds of my audi rs4 rear doors to eventually make in carbon. The drivers door is in perfect shape, but the pass. door has a very shallow indent from a door ding or the like. I am not afraid or new to doing body work as thats what I use to do for a living. My question is this. Is it better to do the body work ahead of time and get it all smooth or can I make the mold and then sand the raised area of the mold that is the reverse of the dent. I think it would be easier to block it down than to fill it up on the actual door. 

It's hard to recommend anything, as availability is always going to vary from place to place. Personally I don't actually have any off-the-shelf epoxy tooling systems available to me here in Aus, not in useable quantities anyway. So when I need an epoxy tooling gel, I blend my own using laminating resin and a variety of additives and pigments. Works very well. Not as nice to work with as the Airtech stuff I've got here, but still good. And doesn't cost the Earth.