So if you modify the whatever.ini file to change the speed (constants.ini file), if you then make the directory structure:

My Mod Name\DataAnd have your constants.ini file in the data folder - then zip those two folders up with an extension of .zip.flmod instead of just .zip - that will be your flmod.

Your "my mod name" will be the name that appears in the mod manager, and simply represents the freelancer folder itself. Basically you build your mod as per the Freelancer directory structure inside your "my mod name" folder, so if you were to replace say - universe.ini, you would stick it inside the folder:
my mod name\data\universeZip up the whole thing by right clicking the "my mod name" folder, and selecting your create zip file (where you can enter a name etc).

If you were to put a script.xml file in, or any other xml file - then you would do so inside your "my mod name" folder.

Hope that helps you out.