Hi Mick
Currently the MegaWrap system only works with non skinned meshes, we are working on the skinned one at the moment. But to do what you want without the wrap feature you would just need to create the morphs for the clothing in your 3d package, and most 3d packages will have a feature to morph clothing along with the base character, for example Daz 3D will do so. So until we get the skinned version done prepare your morphs for clothes as you would normally and when you morph your base character morph the clothing along with it.

If though you are just talking about changing clothing on a base character that doesn't change then you will again just need to build your blendshapes in Maya to suit the look you need, so have one where the sleeves are short, one where the collar is long and export those. Then in Unity you can adjust each blendshape and mix them however you like.

If you are new to morphing/blendshapes then I would suggest playing with Maya to learn how it works and then when you are ready get it into Unity, if you can make it work in Maya it will work the same in Unity with MegaFiers. For changing colors of clothing you will need to do a little extra scripting to change the material params as well as the morph channel values.
Chris

Update: The wrap system now works with Skinned Meshes.