What's a good guideline for setting intended deployment times? Roughly the length of time fuel will last? Twice as much? Three times?
Also, what's the process for resetting a ship's deployment time, after they start to go over and morale begins to drop?
I know it's a bit of a cop-out, but it depends on how much moving the ship will do. For two examples, a gravsurvey ship can be expected to spend the vast majority of its active deployment moving since survey locations require relatively little in the way of survey points, while a geosurvey ship can be expected to spend much more time parked over planets and other large bodies that require multiple hundreds of survey points to scan. The former will thus require much more fuel than the latter over the course of their deployment times. Military ships can be expected, likewise, to spend much more time maneuvering, but may also be operating with a fuel tanker in the case of large fleet operations. So, basically, it depends. I usually start by specifying a deployment time, scaling the fuel capacity to within 20% or so of it, then if I expect the ship to spend a lot of time parked or reliant on external fuel storage, scale down the fuel back down from there. Otherwise, I just look at extra fuel capacity as being a cushion for maneuvering. If your ship goes over on crew deployment time, your crew gets a bit unhappy. If your ship goes over its expected maintenance life, it's still all probabilistic if you get a bad breakdown or not, but it's only a matter of repairing from MSP (assuming, of course, you packed enough). If you run out of fuel in the middle of combat (because you took an unlucky hit to the fuel tanks or because you just ran dry), you're in a bit of a pickle.
As for resetting a ship's deployment time, simply park it in the same location as either a colony with a sufficiently large population (10,000) or a ship with a recreation module. It will go on shore leave, which will lower its deployment time to zero. No extra orders are needed; all you need to do is have the ship moved there. Shore leave, unlike overhauls, can also be interrupted at any time to give the ship new orders.