In the herp world it is referred to as "shedding" or "sloughing" (medically termed "edcysis"), molting is for birdies :w You should have no problems as long as humidity is adequate. The substrate should present no problems at all, but she is probably getting a little annoyed at having her head cleaned constantly
Many species stay beneath substrate almost all the time, some not at all, and some only part of the time, this has no bearing on their shed cycle. What is important is the humidity levels, if it is too low then your snakie will have trouble and it will come off in peices, and some may not want to come off at all. Shedding time is the best time, its always so exciting to see whats underneath the old skin...kinda like opening presents
Take care