Land transportation around Madagascar are long and awful, most would save time by flying via the only domestic airline, Air Madagascar and private planes.
A good suggestion would be to book and pay for your domestic airticket at the time of your international ticket purchase. You would receive 50% discount on the pricey domestic ticket and quoted in US dollars instead of Euros should you buy them locally. Flights are infrequent and often fly twice or once a week, as the planes are small, they get filled up quickly especially during peak season from July – November. All the flights depart and return to Anatannarivo, the capital city which makes it a pain and a waste of a day waiting for your city to city air transfers.
Best to hire a private 4×4 jeep to drive around the various places. The road conditions are so bad that a short 100km could take at least 3-4 hours. Highways and major roads are old pothole ridden and often left to break down. Private car hires are expensive and it cost me Euro700 for a 10 + 2 day trip return from Anatannarivo to Tulear return. As I only rented a regular car, was not able to visit most of the other places and reserves due to the non-existent roads accessible only via a 4×4 wheel vehicle. From Anantannarivo/Antsirabe to Morodava cost Euro$300 (bargained down to Euro$275). Private car hires are easily available in your hotels as most have tie up with travel agents.
Public taxi buses are cheap with average of 20,000 – 40,000 aviary (8 euros – 16euros) for a 12-15 hour ride 400-500km distance. Its a tough ride and often jam packed with people and goods piled up high in the roofs.
Aside from taxi buses, zebu carts can be hired for short distances of less than 20km, extremely slow but effective if you like the scenic view and meeting the locals.