Erm, no. No no no no no.
Sorry if I'm being rude, but this is NOT the way to go about doing things, at least in this case.
The proper way to overwrite old systems is to, quite simply, "overwrite" them. The way plug-ins work is, as no_use_for_a_name said, the original data files (in your case probably Override Data 1, Override Data 2, Override Graphics, Override Sounds, etc.) are loaded first, then the plug-ins are loaded. What happens is any resources in your plug-in that have the same ID number as a resource in one of the data files becomes the resource that is used. So say you have the following syst resources
Original Data File:
128 Sol
129 Centuari
130 Liat
Your Data File:
128 Bob
130 Meh
131 Blargh
132 Whee
Then what'll get loaded when you start EVO is the systems Bob, Centauri, Meh, Blargh, and Whee.
Now, if you want your plug-in to have fewer systems than the original, just replace the other systems with empty systems that don't connect to any of yours. If you make it so that they need a VisBit to be set for them to be visible, that should probably ensure you don't have them showing up in missions.
The method the other people suggested can be useful if you know what you're doing, and if you're working with Nova (only because Nova has so many resources). But in your case, if you're just starting out, and if you're writing your plug-in for EVO, then you should probably use the method I just described. That really is the way plug-ins were meant to be written.
I hope that's understandable. Please let us know if you're still confused.