The most important thing is to replicate the directory
structure from one machine to the next. This affects the path name
for the start page and the output. If your output is WebHelp,
another is that unless you also copy the generated files to the
same location on each machine, publishing will always "Republish
All" by default (a few thousand?), instead of only publishing new
and edited output files (only a few?). (The publishing process
compares old to new in the folder being generated to
on the local machine.)
It's also best if you generate the output to an entirely
different directory that the default !SSL! folder; for our IMS
merged project, we use C:\imsmerge for the source, and
C:\imsgenerate for the output. Each of these folders could be
zipped into separate zip files.
Good luck,
Leon