Did they use the same color uniforms? Could see that getting confusing on the battle field
The uniforms were usually dark (black, dark blue) for both side, but they worn their clan emblem on a small fabric slip on the upper left sleeve.
Anyway, I painted the Imperial troops with black uniform and the Shogunate troops dark blue.
By the way, you can find a short guide about uniforms in the Boshin War on my blog.