If speed is an issue, consider using RFTools Crafters. They are very fast and can reuse the output of its own recipes. You can also put multiple Molecular Assemblers around the same interface, if you haven't done that already.
Issuing a crafting job to a computer works the same way as with regular machines. Just put an interface next to it with some encoded patterns. It has no way to know which recipe is being requested, so you have to make sure they all have unique ingredients. Basically just replicate a Crafter with computers.
I also wrote some documentation on the AE2 components, maybe that's of some use to you: https://github.com/Yepoleb/oc-components-doc