Josh,
The back-end tools like the linker can certainly be a little harder to debug than the C code, but they should be manageable. If you run into problems with the linker, the process is essentially all controlled by the .cmd files linked into your ccs project and the results are available in the generated .map file. These files are worth a read though to demystify the build process and header files.
Great to hear that your lab is looking to use C2000 in the future!