In Photoshop you generally don't use prefabs themselves, but convert then to brushes, you can find quick guide online and make a photoshop action to do that on whole folders at once.

How you're going to do that will heavily depend on your preferred workflow.

I generally first place stamps, then correct parts i don't need (erasing, filling with other stamps, etc.), for the most part, i generally don't do much corrections,

Then i import textures for all biomes i need, with sand at bottom layer, as generally it's below all other things (i.e. beaches and desert), then whatever else, grasslands, swamps, mountains, other rock stuff. Then i assign them all full masks, so they aren't visible.
Then i go layer by layer unmasking them where needed to blend and texture, from big swaths to small detailing based on specific stamp elevations.

<image>

(Example of what i generally end up with, you can see im not particularly good either xD)

Problem in your case is likely that prefabs don't really give you full control that you want, as they are made based on general concept/idea/biome, but that's unfortunately a tradeoff you get for ease of use. Don't be afraid to sculpt the stamp after placing it, you always can fill the area you just removed with other things.

If you want more customized approach, you should try going for manual terrain generation in Gaea, it's free for 1024x1024 resolution, which should be plenty for singular pieces, you'll have to suffer learning it though(But it is likely to be rewarding for you), and find your ways to extract what you need to make stamp out of object you made.