Individual bricks have the notion of points of rotation: centers around which the brick rotates on a given plane. This lets, for example, the various hinges move in a "natural" way. It would be nice to have the ability to set similar centers for submodels, so that they also move in a "natural" way.
At the very least, it would be useful to specify a single brick in the submodel and say "use this brick's centers when rotating the whole submodel". For example, say you had two submodels that represents segments of an arm. Say one segment contains a 481 piece, the other a 482 piece, with the idea that the two segments connect at this hinge. If you could specify that one submodel rotates around the 481 and other other around the 482, it would be much easier to get the arm-like action right in the main model editor.
The existing solution to this is to move the contents of the submodel so that the piece you want at the hinge point is at the origin (coordinates 0, 0, 0).
This is how I always build submodels - I start with the axle, hinge, clip, or other connecting piece, and carefully position it at the center. Then, when you rotate the submodel, it will indeed rotate around the appropriate feature.
A useful trick to help locate the key piece precisely in relation to the origin (since the hinge or point of rotation might not be at the part's origin) is to create a "coordinate axes" submodel you can insert to clarify the exact center of the submodel.
See this post for other related ideas and an example file containing some coordinates axes: http://news.lugnet.com/cad/dev/mac/?n=747&t=i&v=a