The zeppelin parts are all in the main fjords area, so you can fly around and check out wyvern nests as you explore various ledges, etc (there is also one on the small island near the grand knight teleporter shrine).
On this fjords map
the rough locations are marked with an S
. Alternately, from the D2:ED walkthrough
(the locations are the same in DKS),
For the flying fortresses, once you spend a little time running/flying around you should get the hang of them. You could take out the anti-dragon defenses in one area first, then go through in human form (or vise versa), to try to help keep track of where you have explored already. Some of the fortresses are easier to navigate than others.