Again with the tech support questions on OFPEC... ok, here goes...
A shortcut to OFP loading the three mod folders "foo", "bar" and "zoing" would look like
C:\Somewhere\OFP\OPERATIONFLASHPOINT.EXE -nosplash -nomap -mod=foo;bar;zoing
and load addons that are in the folders
...\OFP\foo\addons
...\OFP\bar\addons
...\OFP\zoing\addons
in addition to loading the ones in OFP\Res\Addons (loaded first) and OFP\Addons (loaded last).
-nosplash disables the irritating blooming splash screens on startup
-nomap uses a different method of handling OFP's memory and might help with a lot of issues and inability to use OFP
Learn more about these things by searching the official BIS forums.