Agree with kinnem. It will be seamless once it gets up and running. The first semester's billing can be problematic as the timing doesn't always line up exactly. I "think" that the actual payment doesn't process until the incoming freshmen have passed their physical fitness test (which is done right away). Usually the first semester payment is due before this.
In our case, the bursar's office knew our DS was a scholarship candidate and either had us short-pay the bill or hold payment until the ROTC funds were received.
My memory is foggy but pretty sure of the above.
I have seen many posts here where this question comes up and the recommendation is to call the bursar's office for guidance.
After that first semester, it has never been an issue with very prompt payments by the Navy.