I hope this will help some of you..

0. Get FLMM (Freelancer Mod Manager) and install it.

1. Unpack MyMod.zip to C:\Program Files\Freelancer Mod Manager\Mods
(or wherever you installed it)

2. Open FLSE and load \Mods\MyMod\DATA\UNIVERSE\SYSTEMS\MYSYSTEM1\MySystem1.ini

2,5. You can skip to 5 if you want.

3. Edit the system.

       NOTE : Each time you make a new system or a base in a system,
       it needs to be added to "universe.ini", bases being at
       the beginning of the file, and systems at the end.

4. Save your system INI

5. Launch FLMM, activate MyMod

6. Launch FL Server from FLMM (LAN)

7. Launch Freelancer and connect to your server (LAN)

8. Enjoy!

NOTE: \Mods\MyMod\DATA\CHARACTERS\newcharacter.ini
      determines in which base your character will spawn

PS: If you need more help I suggest searching TLR forums, all the questions
    you could think of have been answered already. Also learning by looking
    at other systems is a good idea ;)