Actually, I may have answered my own question. Let me know if this is correct. This information is from Taco Cohen's Introduction to Shader Programming:

"Since engine version 6.40.5, you can assign materials to (a part of) a model in MED. In MED, go to Edit > Manage Skins. If there is a skin already, click [Skin Settings], if there is no skin yet, click [New Skin]. Check the “Effect Setup” and “Texture” Boxes and choose an effect file (.fx) and a texture file."

This way, it doesnt matter how may textures are assigned to a model, I would just assign the .fx file in the Mana Skins properties.