if you go to marojejy you need to book a flight to Sambava or Antalaha; if you go to Montagne d'Ambre you need a flight to Diego Suarez (Antsiranana). I would organise that together with the flight from Europe to Madagascar.
I dont know Amber Mountains, but i know Marojejy. Lots of Uroplatus, Phelsuma, Paroedura gracilis and tons of frogs. Trails can be steep, especially the last part of the 'trail' can be difficult. Once you are landed in Sambava or Antalaha, you need a taxi or a bus that drives to Andapa (Entrance of Marojejy NP lies on the good road between Sambava and Andapa). Samabava is also a good place to rest for a few days as there are several good hotels.
I'd recommend if you are in this region, go to Masoala, too. You can make a 5 to 7 day walk through the whole Masoala NP, from the coast on the east to Baie d'Antongil on the west. If you are interested, i can give you info of accomodation etc.