There’s multiple ways to pull it off! If you want find control and sculpting you’re going to want to look into a few key things. If you already have locations and such for your lakes mapped on the terrain and you don’t want them to affect it? You can untick the bool, BUT it’s harder to get it to look good that way. It might be better to swap over to Max blend mode, it will allow you to raise the terrain around the lake and still sculpt around it to make it how you’d like.
Then when you want to handle the depth, it’s a good bit of fine tuning. There’s so many things to work with, I highly recommend combing through and playing with them to know exactly how they all work.
We’ll go through a bit in order to make sure you know how to make the lakes deeper/more customized.
The falloff settings will also help you get your cubic lake edges to be cleaner when working if you do keep affects landscape on. I prefer width over angle myself but not always.