68 or 84?
 

Which campaign is the most fun? I'm in the early stages of training on this game, so I'm still mastering the basics, but I'm curious as to whether the 68 campaign is more cat and mouse, with the 84 campaign being more of a case of 'launch and run away'?

That's pretty much it. I spend the vast majority of my Cold Waters time playing the 68 campaign with the Skipjack class. While its true in 84 they do have many more new and exciting ways to kill you, the manifest inadequacy of your weapons (slow electric Mk 37 wire-guided torpedoes or Mk 16 straight-runners) make 68 quite dicey. With the 37 you have to spend a lot of your time very carefully getting into your enemy's baffles to set up a perfect shot (otherwise if he hears the fish he will speed up and out run it) and with the straight runner, you almost have to fire them off in spreads to have any hope of getting a hit, otherwise you can get in insanely close but that is often impractical.

Once you set the waypoint on your target, how do you set it and leave the map without firing at the target?

As far as I know, you don't. The weapon waypoint is only going to stay on the map if the weapon is fired.