I strongly recommend that, instead of trying to understand the C++ code, walk through this Python implementation of the Manbers-Myers suffix array construction algorithm , by hand, for a simple 5 character example.
Because the Python version is only about 15 lines of code, so it's pretty easy to follow.
Even if you don't understand Python, treat it as pseudocode and Google the syntax you don't understand.
Personally, I walked through one 5 character string by hand, and it was enough to help me to understand how the algorithm worked..