I try to take this into account at the foundation level so any settlement is not transmitted to the structure above. This can be done several ways:
1. Try to equalize, as best as possible, the long term dead loads to all the footings, spread and strip.
2. Design the concrete stem walls to span at least 10 feet should there be any localized settlement.
3. For isolated pad (spread) footings, use grade beams to transmit any settlement to other footings.
4. Make sure that the geotech, in his soils report, outlines the anticipated settlement amount and makes any recommendations he thinks should be undertaken to minimize the effects.
5. Over-excavate and place structural backfill for better bearing, possibly less settlement.
6. As a last resort - piling.
I'm sure others in this forum have more ways, but these are the most typical I know.
Mike McCann
MMC Engineering