In our fourth week here and have learned a little bit about getting around independently. On flights, we used Avia Reps plc in London who have been excellent at getting us seats (even when the Air Mad site said there were none) at short notice and applying the 50% discount.
On taxi-brousses down the RN7, if you're starting from Ambalavao or Ranohira there is no station so you can have a long wait. It's possible to pay a deposit in Fianar to get a seat 'reserved' but it's a bit of a hassle. We luckily got Adrien at Anja Reserve to sort us out but still had a 4 hour wait then a 5 hour journey. From Ranohira a local guy who our D'Isalo guide introduced to us sorted us out. He stuffs about 15 people into an estate car to Ilakaka where you catch the taxi-brousse.
One last travel tip, a taxi from Toliara to Ifaty costs 70k Ar and we found this faster and more comfy than the 4x4 that cost 100k Ar!