Hi Will - an "object properties" type mechanism for assigning some basic attributes to objects is also going to be part of the whole object organization batch of work - it should include the type of stuff that you are asking about here.

In the meantime, if you are having some problems assigning materials, you should give the SeparateOBJ.exe utility program a try, you can get that from here:
http://moi3d.com/wiki/Resources#SeparateOBJ_editor

When you run that program, it will let you pick an .obj file saved from MoI, and it will edit the .obj file to break it down into smaller objects which can help make different grouped chunks of the polygon model more easily selectable in certain programs.

That should make it easier to assign materials without needing to select individual polygons.

Like Jonah mentions, for some programs you can just uncheck "Weld vertices along edges" and they know how to separate the chunks out themselves, but some programs won't handle that automatically but do respond better to the additional information that SeparateOBJ.exe adds to the file.

- Michael