I can't seem to find the link to the IRC chanel due to updates so I'll state my minor porblem here:
I have a model that needs two maps but I need it in one mesh.

This has never been a problem because I've just avoided it by detaching polygons into a different mesh.
I also want to color to be more organized.
I have a feeling both of these fall under the catagorey of vertex colors and material ID's. Sadly I don't know how to use them.

select the polys and drag the new material onto them

It worked!
Then Max crashed!
I love you 3dsmax.

Ok, here's the steps:

Enter polygon selection mode.

Select all the polygons that you want mapped to your first map. Then go down to Polygon Properties on the right, and under material, next to Set ID, type 1, hit enter.

Now select all the polygons that you want mapped to your second map. Do the same thing as before, but instead of 1, type 2, and hit enter.

Now open up the material editor. Click the button for the material type (Standard) and change it to Multi/Sub-object. The ID numbers you see correspond to the ID numbers you entered before. The submaterials are where you'd apply the texture maps you want (usually labeled Material #whatever). Click that label, and the usual material editing interface appears.

When you apply the the Multi/Sub Object Material to your mesh, it will automatically figure out which textures get applied to which faces by matching up the ID numbers. I hope this helps.