Based on tips from users, and some of my own preferences:
1) always keep an original untouched version of the existing mesh. Definitely use only one mesh for the site, if you begin to change the levels and they span the meshes, you will have created an unnecessary coordination issue. The choice of keeping the mesh in same file or not is a file size and machine memory issue.
2) I use
S
olid
E
lement
O
perations (SEO) with the building elements as operators to cut away the site to fit the building, then, where you need to add dirt, I add back a mesh and use the original mesh as the operator in a SEO again. I avoid using the "hole" feature of meshes. You can have as many SEO's on the same target element as you need. Remember to set your mesh to solid, if not you can not use SEO's.
3) By following #2, you can now do dirt calculations by comparing the original volume of the mesh prior to and after SEO.
4) By using Meshes and SEO I can have all the drives sidewalks, garden walls, any hardscape in true position, etc. If you need help with roads on meshes, look
here
5)
Why I use SEO's and don't touch the mesh heights or use "holes"
: If you modify a mesh height data point and there is a hole anywhere on the mesh, the whole mesh can "readjust" itself and wreak havoc far beyond the data point you changed. All those roads, paths etc can find themselves floating above or submerged below the mesh.
HTH
Snap
PS my sites are usually less than 4 acres.