If I'm not mistaken, the scripter automatically assigns your ship to Manhattan. Read the "ReadMe" and you should find the time when ShipScripter assigns it to there. I can't remember if it assigns a base code (for example, for Manhattan, it is called "Li01_01", or what.
If it does assign a base code, you can control where your ship is sold by entering the base code of the base you want to sell your ship before you save the file.
If you don't have a list of base codes, do a search here on LR for it; I think there's one here.
Hope this helps; post another question in here if it doesn't.

ok, so whats the codes for the diffrent basses/planets and also were at in the program can you assign the base/planets?

I don't know the base codes by memory - no one that I know does b/c there are too many to do that! Like I said, type "base codes" into the Search box on LR home page, and you will get a DL for it. If you're too lazy :p here is that link :

http://www.lancersreactor.com/t/Downloa ... asp?ID=935

I don't remember when exactly the program puts in the base. Read the ReadMe (like I said!) It tells you when the scripter adds the code. When ever it does (it will automatically put Manhattan's Li01_01 in there), you can change that code by highlighting that Li01_01 and pasting the code of your desired base(s).
Then continue as the ReadMe says.