That's sort of what I do. I make and play on 3d terrain of 1.75" hexes.
After arranging/setting up my table, I then Profantasy's Campaign Cartographer 3+ to then make a map of the table. The Added benefit of using CC3+, is it really helps out during play to track
Line of Sight, as I use the software to snap lines to the centre of Hexes, and I can then zoom if needed to see if the Line clips a hex or not.


I mount the Trees on magnetic bases so they can then be removed to place a unit into the hex, the Trees are Dark for Heavy/Light for Light, and the base itself is colored Light/Dark as well.
For my Buildings, as can be seen on the map and the table, I have also color coded the roof to allow for a quick visual queue as to it's level. This works especially well for those buildings that sort of straddle the edge of two levels. I just pick one, paint it that color, and forever more it will be that level.
The Color/Level relationship is:
Light Grey = Level 1
Dark Gray = Level 2
Light brown = Level 3
Dark Brown = Level 4
Blue = Level 6
Past that, I have yet to decide on a color scheme, but as I get larger buildings, I'm going to need to settle soon
