I get a lot of Google Search hits for this information on SyncToy, so here it is. There is actually a separate executable for running command line options called SyncToyCmd (brilliant!).
Anyway, here is the info.
Usage: SyncToyCmd [-args]
All arguments are optional.
-R Run all folder pairs that are marked as Active for Run All.
-R<name> Run the named folder pair only.
-? Display this help.