Organizing files?

Hey guys, kind of new to PHP and CodeIgniter (and programming for that matter). I have been getting my feet wet with CI and created a few separate "websites". I have a fundamental question. Is it ok to have different sites within the same CI framework? What I mean is, is it ok that after playing around I have accumulated multiple non-related models, views, and controls intermingling in the same file structure (for example site "A" and site "B" both have separate folders under my CI "views" folder.)

1. Is it ok to use only one copy of CI for all websites.. on my localhost.. on a server?
2. Or should a fresh copy of CI be used for every new website.. on my localhost.. on a server?

Thanks in advance! Hope I was clear on my question.

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