You can think about it like this: if you want to get a complicated part made in a material like silicone, you'll need something to form that material - a mold. However, just printing a mold directly on a Makerbot won't work for a lot of shapes because they just don't want to come out of a hard plastic shell. So, I go a step ahead printing molds in plastic that, when poured in silicone, make molds that get me the final shape I want. This makes it easier to get precision parts without loads of manual labor, cleaning up seams, and flashing.
Coat the insides of your 3D printed molds in wax. This will help the final part pop out of the mold easily, in addition to sealing up any little cracks that would allow liquid silicone to pour straight through the print. Fill all the molds to the top with Smooth-Sil according to the manufacturer's directions. This video gives a good introduction to mold pouring if you haven't given it a shot before. Just pour in a thin, even stream starting the pour at the lowest point of the mold, allowing the wave of liquid that rises up to push any bubbles out.
Once the molds are all poured, wait about 8 hours to de-mold.