Glad you like the asset 
I’ll do my best to answer your questions.
It basically boils down to keeping the grid in mind while designing. Your rock does not necessarily need to be a blueprint. It could just be a static mesh. But you proably want to scale most things so that they fit fairly well onto the grid. For square grids this is super easy, as you can just use the default UE4 grid snapping. For hex grids it will take some more testing and moving things around.
As long as you understand how the grid works you are pretty free to design the map as you want. For natural looking scenes you probably want to use the procedural grid systems. Namely the automatic heightmap generation using line traces and automatic wall generation through (bTraceForWalls) in BP_GridManager. After that it is a matter of having meshes you want to be able to walk on block the PathTrace collision channel, have meshes you want to block movement block the WallTrace collision channel and have meshes you want to occlude vision block the RangeTrace collision channel. You will want to play around a bit with how your meshes collision is set up for this. In many cases the default collision geometry of your meshes might work fine, while you might in other cases want to add new collision boxes to fine-tune your setup.
You’re in luck. I very recently made three new videos on using custom skeletal meshes for units. Take a look:
You too, and no worries!