If you open FLMM then click on the 'how to make my mod FLMM compatible' it will give you a list. One way is just to put the files you have changed into their respective folders in the FLMM mod folder (using the same structure of folders - ie for a modded shiparch.ini, make a folder of your mods name in the FLMM mod folder, then put the shiparch.ini in the directory structure for it - ie make a DATA folder, which has a SHIPS folder in it. THen put your shiparch.ini in the ships folder). The best way is to make a script for small mods, and that uses XML scripting - but there are examples of how to do that in the FLMM 'how to make my mod compatible' section. Really see the FLMM mod guide i mentioned though - explains it all there.
Chips