Naaah, you can use skills all you want without anything breaking, the only downside to using them is that, as I recall anyway, they can't increase your weapon level, so you still need to use at least one basic attack during a battle for a shot at that. Speaking of those levels though, be careful when unequipping weapons, because you will lose ALL of your levels with a weapon if you remove it. Kind sucks if you remove something like the Chalice. X_ X
Stuck in the sense you can't reach an exit or in that you cannot defeat the boss? If it is the former, you can lose to Forneus, or any other abyss lord that isn't Byunei on Gwayne's back, and get teleported back to one of the cities (as I recall anyway) and you can dodge most of the running fishmen in his castle by hugging the walls if they were giving you trouble. If the issue is the latter, I'd say to knock off the other three first, as he's the most consistently difficult of the four, especially early on with Squall's silly high chance of changing battlefield element to water and healing off a lot the damage you do to him each turn. You can also try running the Genbu or Tiger's Cave formations when fighting him to cut his damage in half if your damage is high enough and just surviving is the biggest problem, though neither helps with Maelstrom's IK chance.