Neither really, although 'frequently' is an odd word to use with 'going to school'. 'Going to school' is something you should always do, and it makes sense to refer to how often you fail to do it. 'Frequently' is more natural to use with things that you are not expected to do, but do anyway. I would say ( in decreasing regularity) Always 1 2 Rarely Never In other words: 1 is more frequent than 2.

Neither one means "He frequently goes to school". To say that in English you say exactly what you wrote: "He frequently goes to school". Both of the sentences you wrote mean about the same thing. They both mean he skips school often. Rearranging the words makes a small difference, but not a big difference.

1 sounds like he does goes to school but often skips it and 2 sounds like he barely ever goes to begin with.