The choices? Let's say you see a Flamethrower cube. Obviously, you can decide to walk into range and die. Preferrably, you would also find a way to destroy it, or leave it be and mark that area off in your head as unsafe.
Another example: you can build a resource farm by placing Water Portals and devouring what comes out of them, then spend those resources on cubes it can afford. Scaffolding is always useful, in both getting away, and getting to things, but you can also set up a small base of your own, complete with healing machines, fragment farms, grindstones, and the Charge systems that may or may not be needed to power those. But if you're like me, you're probably going to die running into something you knew would kill you, before any of that, lol.
In terms of deciding what to break or not, I would often deliberately keep around certain fallen cubes even if they were dangerous to me, as I knew they would also be dangerous to other cubes that might be worse. Or a passive cube might be useful as a wall to build my foundations on. I'll destroy a cube if I decide it not worth the risk keeping around, or its fragment value outweights it protection.
There's of course another playstyle where you don't build anything at all - it's pretty risky, with no rewards, but nothing's going to stop you.