So after what was pretty much a lost weekend due to Dreamhost screwing up the servers all weekend long I was able to finish off most of the Manufacturing functionality today. I've still got to make it actually use up materials and do some more polishing, but right now I can pick an item from a list and have the colony start working on it.
So far I've worked it that you will build Factory Modules at your colony. The module can have a number of build queues equal to it's integer level. So a 1.2 module can have one queue, and a 2.7 module can have two. Once you start building, any needed materials are moved into "Reserve" status, so they still take up space in the Warehouse, but can't be used for anything else.
If you choose to build 200 Structural Units, then it will build each one individually until they're all completed. Partial builds will be available as soon as they're completed, so if you start building 200, then about five minutes later you'll have 1 new Structural Unit in your warehouse, and 199 left to build.
I've also nailed down the item hierarchy. It will consist of four levels:
I : Raw Materials (example: Base Metals Ore)
II : Processed Materials (example: Processed Base Metals)
III: Manufactured Components (example: Electronics, Structural Units)
IV: Manufactured Items (example: Jump Drive, Laser Cannon I)
Each level will be composed of 1 to 3 different types from lower levels. So Processed Base Metals will take 2 Base Metals Ore. There will likely be Technology that will lower this ratio. Structural Units may take 1 Processed Base Metal and 1 Refined Hydrocarbons.
Here's a screenshot of some build queues in action.