1. There isn't any program that's a magical, "create whatever I want in Freelancer" solution. No matter what it is, modding FL requires that you understand the scripts that run underneath it all... and that requires that you do some reading, experimentation, and some hard work.
2. Like all powerful tools, FLE can work very well-
if you know what you're doing with it . You cannot just expect to sit down and whip out Systems, though. Chances are... your problems with your new System(s) are being caused by coding errors introduced because you used FLE incorrectly. Yes, there are several versions of FLE around... and the latest version is considerably improved over previous ones, so get the latest one. But it's not perfect, and it's certainly not going to do what you want if you do not know how to get down-and-dirty with the INI scripts that it creates. In short... FLE, while useful, is
not a substitute for coding skill .
So... I would advise you to go back to Square One. Start by downloading the FL SDK (version 1.5 is the latest)... and then try a few
simple experiments, such as changing the position of Manhatten, the angle of its docking rings, etc.
Once you understand the basics of INI editing... please take awhile and study the INIs that are essential to working with FLE, namely:
Systems.ini
Mbases.ini
YourSystemPrefixHere(this could be anything).ini
Goods.ini
Weapon_good.ini
And then the detailed underpinnings, such as the scripts for Bases and Rooms.
You cannot just download a tool and make a great mod... we're all hoping that you have what it takes, but if you expected it to be that simple... you're just going to be disappointed. Think your task through, grit your teeth, and get reading- you will be much more likely to succeed, believe me