Here are two ideas just to throw out there, and I'm using this recipe as inspiration: http://www.erinsfoodfiles.com/2010/04/lincolns-red-velvet-cheesecake-cake.html
1) Simple: Make a red velvet cake batter, but fill cupcake liners only 1/2 way and bake for about 1/2 the time (or whatever it takes to get them baked completely). Let cool, then top with a generous portion of no-bake cheesecake filling (something like this: http://www.kraftrecipes.com/recipes/philadelphia-no-bake-mini-cheesecakes-53063.aspx
) and a creamy dollop of cream cheese frosting.
2) Complex: Bake a red velvet cake in a sheet pan (1/2 sheet, full sheet, depending on how many cupcakes you're making and the size of pan you have), then bake a cheesecake in a sheet cake pan. Here is a discussion about how to do it: http://www.cheftalk.com/t/68193/mini-cheesecakes-without-a-special-pan.
When both are cool--and you may want to slightly freeze both for easier cutting--cut each with a round cookie cutter so that you're working the same sized pieces. Use the cake as the base (obviously), then top with a layer of cream cheese frosting, add the cheesecake piece, and swirl with more frosting.
Please keep us posted on how this turns out--it sounds like it has the potential to be absolutely amazing!