You've got the right forum, FLMM tells you how to if you goto help

Quick and dirty way:
All the files you have changed / modded (includes systems_shortest_paths etc - everything that you have changed.....)
Create a folder in the FLMM mods folder (mods folder inside FLMM directory) called by your mod. Next, create the folders containing files you have changed in the games directory structure (ie - you make a change to universe.ini, LI01.ini and Li02.ini, then make a data folder, inside make a universe folder - in there make a systems folder containing LI01 and LI02 folders)
Now put your files in their respective folders. This is cause FLMM will look at what folders have what files, and change them when acitvated with the games ones (making backups as it goes along).
Hope that helps, and make sure you include EVERY file - no matter how small (including rooms, base.ini etc)

Thanks chips, will it hurt to include all of the dll files with the ids number info, I don’t know which file deals with which item.

To include all the dlls that you have made, put em in the exe folder along with the freelancer.ini containing the link to those! ie -- for this part:

[Resources
DLL = InfoCards.dll ; Contains all infocard text resources
DLL = MiscText.dll ; Contains other bulk text resource: rumor, offer, and mission text
DLL = NameResources.dll ; Contains names of things, primarily.
DLL = EquipResources.dll ;Contains names of equipment (in string table) and infocards for equipment (in HTML resources)
DLL = OfferBribeResources.dll ; Contains random mission offers and bribes
DLL = MiscTextInfo2.dll ;Contains MP UI elements as well as other misc. text
DLL = te_mod.dll ; Custom dll <-- my own custom one - too lazy to remove, you get the idea......lol
Strictly speaking you don't have to put the dll files into the EXE folder, just leave em in your mod folder and they get put into place, but it never hurts to make sure eh?!