Having Leia on a Corvette would also help with this dilemma. As long as she is within 5 of the AFMk2, you can use the Corvette to plot a nav command when you need it, and use Leia's ability to switch the top command on the Assault Frigate to a Nav Command as well.
How often do you Navigate?
Depends on strategy. I typically don't use more than 2 total nav commands out of 6 as Rebels.
Imperials, that's another story wave 1 and only one GSD. That's more like 4 a game.
I use Navigate a lot. I feel that Navigate is the most powerful command for the following reasons:
1. It affects how much damage you'll deal and how much damage you'll be dealt due to range and ship arcs. More so than Concentrate Fire.
2. It affects how you'll perform a lot of your objectives. A lot of them requires you maneuvering very carefully in position.
3. The easiest way to lose a ship, aside from hanging out in front of a VSD or ISD, is to fly off the board. Navigate prevents that.
4. It aids in either causing or preventing ship collisions as well as managing asteroids and debris fields.
5. It can put some distance between your ship and enemy squadrons.
No other command affects so many aspects of Armada gameplay as much as Navigate.
I increasingly find myself using Raymus on Tantive IV to give navigate tokens to my other ships. I've also thrown nav teams on my larger ships- when they use the command and token together, having an extra two clicks of yaw can lead to some pretty radical repositioning.