(1) What plugin making software are you using? ResEdit/NovaTools? EVONE? MissionComputer?
(2) To create a new system, you need to work with syst resources. By the sound of it, you are only working with spob (space object) resources, which are the resources that control planets and stations. Syst resources are the systems themselves.
(3) To overwrite Nova's systems and create your own, simply create syst resources with the same ID number as Nova's resources. Plugin data is loaded after the data files, so your data will overwrite the Nova scenario's data and your own systems will appear instead. If the number of systems you are creating is smaller than the number in Nova, you may need to create lots of blank systems to overwrite the remaining Nova systems.
Sorry, but I need more info to be more helpful. 
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(url="http://"http://www.mazca.com/")Mazca(/url) , Moderator, (url="http://"http://www.AmbrosiaSW.com/cgi-bin/ubb/forumdisplay.cgi?action=topics&number;=9&SUBMIT;=Go&urgaylol;=yes")EV Developer's Corner(/url)
Go get your knife.