@ Xeno, "visit = 0" means it doesn't show until you find it, "visit = 1" means it's always visible, what you want is "visit = 128" this means it will never show.
@ Xerxas, 2/3 weeks ago I helped a noob who was trying to do the same as you.
The problem is trying to remove the vanilla systems, because of the way FL is coded you can't remove all of them. This leaves you with two choices either do a Total Conversion (TC) or block entry to the vanilla systems.
The TC method is long and complicated as you have to keep all of the vanilla nicknames and re-use them for your mod, take a look at Freeworlds 1.66 to see how to do a TC but be warned this took the mod
team 18 months to complete.
Blocking entry to the vanilla systems is always the best bet for small mods. Do as Mace says and change the "visit =" to 128 for all of the vanilla systems in the universe.ini and then move them all to the edges of the navmap. This will give you a large area to play with, now create 1 system with 1 base just to get you started, it doesn't even need to be populated, just have rooms. Now copy the files from the OpenSP mod of your choice into your mod, change the start location to match your system and base (M13.ini usually) and you should be up and running. As long as you don't have any jumpgates/holes from your systems to the vanilla ones, nobody will be able to get into them.
**shuffles of with a new headache**