Basically, if you have one site toposurface, and you cut it with pads in different phases, then an ‘outline’ around every single pad appears in the creation phase of the toposurface (they affect the topo backwards in time).  It looks ugly …  Additionally, there will be ‘holes’ cut in the toposurface for the pads.

I recently handled this by making a Design Option Set for Topography, then for each Stage / Building Option combination, I added the entire site Toposurface.  From here, I could use model groups to transfer pads between the different options / phases, while still retaining their size and position and editability.  It was a pain to set up, but once configured properly (with views etc), it seems to work ok.

The most ‘logical’ way to configure it would be:

  1. Make a Design Option Set
  2. Make an Option called ‘Existing’.  Add your original / untouched site topography here.
  3. Duplicate the Option, call it Stage 1.
  4. Make all the Stage 1 pads, then group them.
  5. Duplicate Stage 1 topography option, call it stage 2 (the grouped pads will come through).  Add additional pads in Stage 2 option, then group Stage 2 pads and the Stage 1 pad group (forming a nested group.)
  6. Rinse and repeat

I never said being a Revit pro would be easy.

You can read about the problem at:
Re: Building pads don’t seem to respect phases. – Autodesk Discussion Groups

You know when you have two pads meeting at a common edge, and then Revit for some reason shows this tiny sliver of created topography between them?

Try this:

  • Set the two Pads to have the same ‘Level’ and ‘Height Offset from Level’ property values
  • If you need to use slope arrows, you should still be able to get them to work upwards or downwards from this particular level

This tip worked for me – I hope it helps you.  I’m pretty sure that there are still situations where things still just won’t quite work…but for the time being, Revit Wants you to set adjacent Pad levels at the same value.

Tip via this thread
Pads Pads Pads…oh and there’s a problem – AUGI

Two tips that I found of particular value:

“…click on Graded Surface… If you don’t do this first step, you will not get Cut and Fill counts when you create Building Pads.”

and

“Be sure that first you select the Topography, then click on the Building Pad Button on the Massing & Site Tab. Otherwise, the Pad will be created, but sometimes (I haven’t figured out why and how this happens) the Cut and Fill will not be reported on the Topography Schedule.”

Read the whole post:
CAD addict: Revit: Using Building Pads Properly – Part II