What you really want to do is index all of the sections into one database.
Just do each one separately with it's own set of options. You may want to
use the -j option if you're not already. You'll also probably want to use
-O to prevent it from remembering urls across sessions.
gw -dthedb -wipe
gw -dthedb -O -noindex ...options_for_1...
http://site1
gw -dthedb -O -noindex ...options_for_2... -jhttp://site2/somedir/
http://site1/somedir/
gw -dthedb -O -noindex ...options_for_3... -jhttp://site3/somedir/
http://site3/somedir/
gw -index
You'll want to place all of your commands into a short script so they
are easily repeated in the future. -rewalk will not work in the above
scenario.