I too use Display Fusion, and yes you can specify different folders for different monitors for it to pull wallpapers out randomly. It's very important for me since my main monitor is 4k, and my second monitor is 1920x1200 in portrait, and my wallpapers are REAL DIFFERENT per monitor size and orientation wise.

I use Display Fusion to handle my multiple monitors, I'm at work so can't check; but, I believe it may let you use different folders per monitor.

I recommend Digital Blasphemy. He creates all of his wallpapers using 3d modeling and rendering tools, but plenty of them look like nature or space photography. Personally love the style, but I suppose it's not for everybody.

Anyway, he tenders all of his work in a variety of resolutions and aspect ratios; should be possible to find versions suitable for each monitor.

Wallpaper engine on steam