Hi Stan,
Without seeing some code I can't be very specific, but here are some thoughts.
The variable system-system-spacing controls the distance between systems (it can be set in a \paper block or a \layout block I think). I think you have to set it for a whole score though, that is, you can't change it on a per-system basis (but I'm not 100% sure, someone could correct me on that). So one way to accomplish what you want would be to have a separate \score block for each section, and increase the space between scores (with the score-system-spacing variable in the \paper block). If you don't want to put the various sections into their own scores then you could do something hackish like placing something transparent underneath a system to force more space between it and the one underneath.
hth,
Kevin