Yeah, this is basically something you'll have to do as you get to exploring more, as the lack of any ingame map will become a major hindrance as you start to progress downwards. Beacons are a Godsend for helping get a sense of the area. Also, use them to mark zone transitions, as some areas are safe, and others house gigantic monsters, and knowing when you're coming up on a monster area will help remind you when you need to be alert.
I did the same thing at the beginning. But the seafloor actually acts as a good shield for some of the bigger aggressive species that can really hurt you. If you're in open water and certain species set on you, you are completely boned. If you are close to the seafloor, you can throw a juke and they'll tend to peel off before they hit the ground. And then you can book it right out of there and try and hide behind a rock or something. The seafloor is also one of the most telling indicators of what biome you're in. If there's lots of red grass, you're OK. If there's giant mushroom trees, also basically safe. If there's lots of sand and not much else, well, that's a sign that you might want to be somewhere else. You can't see any of that from near the surface though, so you might unwittingly wander into a very dangerous area with no visual cue.
I tried building a base in the same location.
Grapple plus three jump jets is the best. It's fun and it makes the Prawn Suit nearly as fast as a Seamoth! All that extra boost power means you'll almost never have to use the hang-off-a-cliff-while-your-boost-recharges exploit.
Getting in and out of the lava zone is kind of a pain in the ass, especially as the Prawn Suit is difficult to move in even upgraded with a grappling arm and jump jets (if you don't have the grapple arm yet, don't even bother with the lava zone until you do). Frankly, I would recommend trying to do all of the lava zone in one go without returning to your base / sub. So that means you're going to want a LOT of food and water (focus on the most efficient use of space; nutrient bars and large waters from a water purifier). You should go in with a fully charged power cell and bring another with you as well. You won't need things like your flashlight or laser cutter, but a Seaglide is important if a Warper pulls you out of your Prawn Suit, and the repair tool is absolutely necessary. The Stasis rifle can help, but frankly, you're better off just learning how to haul ass in the Prawn suit with the grapple arm.
Here's a guy who did it roughly 4 times faster than it took me to figure out how to build a SeaGlide (video contains spoilers, obviously):
I'm still in the middle of doing all this, but I definitely think it's worth taking the Cyclops down there. It allows you to take your time more, since you can grow food/water on board, and it prevents you from needing to go back and forth a long distance to it to resupply, craft new things, or just take a break. The whole sequence feels like it was designed for the Cyclops.
Reply to spoilered question:
You can absolutely do this on an XInput controller. I did it often. I think you have to hold down on the d-pad or something.
No. You might be able to save during the final sequence, but I don't know why you'd even try. It's pretty obvious when you're about to end the game, and then afterward you can just resume from your save before that.
