I know you say you fixed the problem, but I can't let this sit.
What you do to install the mod is, in this order:
Find the folder you downloaded it to. (Do this by right clicking it and then clicking "show in folder" or "open folder" or something.)
Paste it into your Besiege mods folder.
Then you just run Besiege. Not the mod, Besiege. If the modloader was installed correctly, the mod content should be present.
I don't know what sort of modding you did before, but almost no mod ever requires you to run it. What game were you modding?