I want to make my lakes surrounded in stone and sand but the paint tool will change my water into sand and stone 
I’d love an option to ignore water when painting the terrain.
You could try putting the water in last, or selecting the water and moving it out.
I’ve run into this problem too. It’s pretty annoying.
The paint tool, is to strong 
Sometimes i want to paint the terrain, with more than one terrain aswell, like “sand and grass” or “stone and grass” but then i have to first put grass, then i have to make the brush as small as possible and move quickly over the grass to make it how i want it
This is why my beaches are ugly/cliffy. We need an easier way to put in water (Where’s the flood fill plugin?). If you build the beach first and then put the water in, the water replaces the sand. I suggest making water NOT replace the material that already occupies the space. Or what the OP said.
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The old terrain tools still exist in a place with smooth terrain, you just have to add them back to the plugin row. I’ve used the flood fill with smooth terrain, although you have to be careful because I think it will go through thin terrain.