Do the Tm30 in Nonthaburi (or have your landlord do it), make sure to get the slip. Do everything else in Bangkok since your school is in Bangkok. There is no problem, as it's very common to live in a different province to where you study or work.
2 exempt entries overland per calendar year for SA citizens. In theory, arrivals by air are unlimited, but if officers suspect that she's living here, she may get refused. Try to avoid this by carrying a ticket back home, 20,000 baht in cash and proof of accommodation in Thailand.