Tear off a piece of cardboard that will allow at least an inch around each edge of your prototype. Lay the hold on the cardboard and stick it with two toothpicks from the backside to make it stick. Now I need to stress the important parts of applying the silicone. Dab it slowly and evenly over the entire surface making sure all the small pits are caught in the mold. Also make sure your layer is at least 1/4" to 1/2", or your mold will tear after the first few uses. As an option here, you might want to try putting the silicone tube in hot water for a while before applying it. This will make it less viscous and help reduce bubbles.

If your hold has a positive area, an area incut that will require torqing of the mold to remove the hold later, reinforce this area with extra silicone. There are several methods to making molds, but this is the cheapest reliable way I've found so far. Some suggestions I've read include adding mineral spirits to the caulk and painting this on, or putting the caulk container in hot water to make the caulk less viscous. Again, let me know what you find.

Let the mold cure for a while (usually a day or two). Test the outside to see if it feels squishy. If it squishes, give it another day. Once it is hardened, carefully remove the cardboard from the bottom, slowly pop out the prototype, and rinse out the inside gently with water. Your mold is ready.