I would suggest you stay either reasonably near the main part of Sousse or near the marina in PEK. That way you can get a taxi or tuktuk from one to the other but each area has its own charm, whereas if you are between the two it can be a longish walk to either. If you want to explore independently, the train and bus stations are near the port and Medina in Sousse. Have a look at the maps below to give you an idea of where the hotels are.

http://www.holidaymaps.de/afrika/tunesien/region%20monastir.html