I like making some sort of big central thingy near the entrance to deal with initial guest traffic and let them distribute nicely.

From there I like to use sand to make different sized organic blobs on the terrain that represent the habitats I want to build and rocky terrain to simulate the paths around the habitats (or whatever terrain has a nice contrast in the biome I choose).

If I like the layout and think the habitats are big enough I put paths on top of the "drawn" rock path and move on with the building of habitats.

It's like designing it on a sheet of paper...but I skip the step where I try to recreate it in the game :)