yeah, waves are a thing sadly. They will ruin everything you do on your ship. The way I found to work around it is to sail away from Vell's Realm until the mini map says Margoria, no further. Hopefully the waves willnot affect you here. 👍

I understand waves being a thing, but what I'm describing is that I'm underwater UNTIL I move my boat, and then it only lasts a little while until I'm underwater again. Every time I want to shoot cannons at Vell I have to first move my boat forward or backward. If I stand still I can't fire above the water *at all*

Unfortunately that's a thing and I would highly recommend creating a feedback thread in the feedback forum regarding the bugs you've encountered. Once enough people support you, perhaps send in a support ticket and link that thread that you created and see if you can convince PA to do something about it. Those are all ongoing bugs that never got fixed. We really do all want ocean content to be fixed and improved. You'll get my +1 support when you do :)