Exactly.

Some mods for BI (Like "The New Shadow") also put their modfolders inside a subfolder of the "BI"-folder (which, in fact, is nothing else than a modfolder itself ;) )

These mods each can be launched by simple use of the command line by adding -mod:MODNAME at the end of the target line.

E.G.
-mod:napoleonic for "Napoleonic Warfare Mod" or
-mod:bi\ci for "The New Shadow"
EB would work the same way (-mod:eb), but with TrivialScript (which everybody uses, I assume) things run even more easy ;)