I do not completely understand your question but here is the general configuration for Issue Type Schemes.
In older JIRAs (as late as 6.1 I think, but I am working from memory, and my memory is not exactly great), the default issue type scheme automatically held ALL issue types, and JIRA broke in interesting ways if you tried to remove them via hackery. There really was not anything you could do about that.
In later JIRAs, you can remove them, although I think they still get added automatically. So, the question now is what version are you using?
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