Hello Clint -
Sadly, in TestStand 2.0.x there is no handy tool for bundling cfiles and DLLs, (TestStand 3.0 is another story) but yes, in your case you're going to have to comb through your sequence files and see what you need.
Take your matlab files, the c-files that call them, any support DLLs those c-files will require as far as libraries/linking go. If you've been running your CVI adapter in 'external process' mode, you'll want to toggle it to 'in process' and test things before you deploy to make sure that linking and such works. Also, if you haven't built DLLs out of your C code for you step modules, you may want to in order to protect yourself from tricky-to-debug link errors that can crop up with C or .OBJ files from time to time.
Good luck,
Elaine R.
National Instruments
http://www.ni.com/support