I know this is a few years after your post, so you have probably already received an answer in some way and have long since completed your mini, but based on pictures from the 3 different shows, it appears that for military units like the SGC and Icarus base personnel, command patch goes on the left shoulder, specific unit and air force patches on the right. So for the SGC, you have the Earth home symbol patch and on the right is the SG-1 patch. For SGU, the Icarus base patch on the left and whatever air force patches on the right, since I don't think they had SG unit designations. Atlantis was different since they were mostly a civilian operation, so they'd have the flag for their individual nation on the left and the Atlantis expedition on the right. I would assume that for Phoenix site personnel, it would be similar to the SGC where they'd have the Phoenix patch on the left, and their specific unit designation patch on the right.
If you didn't paint the mini, I hope this helps. If you did, then I hope you found it helpful in some way.