The way I foresee it working is as follows: Two or more companies can form a brigade. If two or more companies exist within an organized brigade that belong to the same regiment, then a partial regiment can be formed and someone can either be elected or appointed to command the partial regiment from within the brigade. If a brigade wishes, it can then place itself under the command of a division HQ to be organized with other brigades. The role of the battalion as I see it should be used within brigades and not have any official status.
So here's a fictional example:
10th Tennessee Company A and 15th Alabama Company C join together to form a brigade. Some time later, the 10th Tennessee Company F joins the brigade. This means the two 10th Tennessee companies (A and F) can join together to make a partial regiment, the 10th Tennessee. I use the term partial because other 10th Tennessee companies could be formed and could have decided to join other brigades or remain independent. Furthermore, the commander of the brigade may decide to detach 10th Tennessee Company A from the 10th Tennessee and form a battalion with the 10th TN Co. A and the 15th AL Co. C mid battle. This wouldn't change the organization of the unit itself as but would just be a mid-battle modification to the structure as the brigadier commander sees fit.
That is how I would like things to work right now, going off of how the community is already organizing. The developers may choose to do something different.
Edit: Looking at the beginning of the thread, it looks like Hinkel initially laid out something a little different from what I proposed. Take a look at what he said to get a rough idea of what the developers are going for.