You'll have to go into Sousse to pick up the train, metro or bus to get to other places. The 'fun' way is by either the Noddy Train or tuk-tuk. Both of these will take you into Sousse and will return you to your hotel, you can pick them up from where you got off. When you get off, turn right, walk to the bottom of that road and you will be right in the centre. The Soula Centre (fixed price shop) is across the road to your right with the Medina just behind it. You will see the Port (and probably the Pirate Ships) in the opposite direction. Walk right past these to the end of the road and you will come to the metro station - for Monastir, Mahdia etc. The bus station is by the Medina walls - just ask and anyone will direct you. If there are 2 or you the taxis are really just as cheap as the Noddy or tuktuk (and quite a bit warmer). Always agree a price with a taxi driver and you certainly shouldn't pay more than about 6 dinars from PEK to Sousse, though prices did seem to have gone up a bit when I was there last month. Ask directions for the main train station to Tunis etc. unless you are have a taxi. If you are considering using the trains a lot, think about getting a Carte Bleu which is incredibly cheap. Have a look at the following:
http://www.seat61.com/Tunisia2.htm#Fares
Monastir is well worth a visit. Do try and see the Mausoleum of the previous president, which is absolutely stunning. Have a look at my report "Jenny, Frank me and the Pirate" on here if you want a good meal. Mahdia has its devotees but there isn't very much there, particularly at this time of year. I quite like Tunis and Sidi Bou Said is beautiful - there is also a lovely cafe there called L'Aetita Svede run by a Swedish lady and her Tunisian husband which serves every kind of tea imaginable and cakes to die for - at least it did when I was there some years ago and apparently it's still there. El Djem is the oldest coloseum outside Rome and is worth a visit.
I hope this has given you something to think about, and I haven't even mentioned the Sahara trip which you can't really do independently as it's a minimum of 2 days and you do need a guide, but you will find a lot of reports on that on HT.
Problem is, you keep raising all these questions and when I start to answer it just makes me wish I was there now, instead of freezing here in Essex.