Anders,
I have been toying with the idea of doing molds of different stuff for several years now. I'm not an expert by any means, but I think I might be able to help you out in getting started. For molding and casting a very important tool to have is a vaccum/pressure chamber. This useful, though somewhat exspensive tool will help reduce the headaches to come. Once your masters are in place, de-air your mold material in the vaccum chamber. This will reduce the likelyhood of air bubbles and or pockets from forming around the master. When you are ready to pour your resin, do so, and then place the entire piece into the pressure chamber. What little air there is remaining in the mold and/or resin will be forced into the very middle of the piece, where it should be of no problem.
To make two part molds I use putty, namely Crayola brand, although you can use a variety of materials. I will roll out what I think I am going to need and add about 1/2-3/4 of an inch on either side of the master. I then imbed the master into the clay and smooth out any uneveness that is readily apparent. I use Legos for the box as they are easy to assemble and disassemble. I then add locating marks or pins with a piece of dowel by pressing the dowel into the clay. I add several of these as I want the mold to be a steady as possible while pouring resin. These will serve as alignment guides for the second half of the mold. Once all is ready, I brush on some mold material (RTV) onto the master. Once it is completely covered, I pour the remainder of the RTV, then place it in the vaccum chamber and de-air the mold again. At this point I will gradually let air back into the chamber, and then leave it to cure completely. Repeat the process for the other side of the mold, being extremely careful not to remove the master from the already poured RTV. Apply a release agent to the already poured RTV, turn the mold over, add the Lego border box again, and pour your second half. Vaccum chamber again, and let cure.
Once the whole shabang is cured carefully demold everything and cut in some pour spouts and air vents where needed. I have been casting stuff now for many a year now and have learned alot, mostly through trial and error. The biggest problem I had early on was the 2 part mold. Finally after finding the clay issue, things began to turn around. With the addition of the vaccum chamber and the pressure chamber, things really began to look up. The $$ for the chamber is a little high, but if you are serious about your venture then it will be a good investment. You might also want to look into spin casting, I believe this is also along the exspensive side of the house. I dont know much about it, but have seen some pieces that have been spin-cast and ther results are impressive. Hopefully this will help you out. If you need any othe information just drop me a line. "Q"