To add to Andrew's explanation; if it works for you in the miniAudicle then you are almost there. The thing to realise is that the mini uses one or a few windows to contain the ChucK code. We sometimes call these "editing buffers". These buffers contain code and they are analogous to files. Where we would tell the mini to run the code in one of these buffers we tell plain ChucK to run the code that is in a file that was previously saved.

Code goes into files. These files then get send to ChucK. We don't (typically) send the code straight into ChucK though we may use a editor like the Mini to take care of the link for us. The process behind the scenes is the same, the Mini just makes it more convenient. There is one downside to these buffers that "pretend to be files"; if you would crash the Mini because you crash ChucK then you also lose all unsaved buffers while you won't crash plain ChucK in a way that makes you lose your files on your drive (at least I never heard of this happening)-

I hope this clarifies, don't hesitate to ask more; both ChucK and a terminal can look a bit intimidating at first, especially if you are trying to get to grips with both at the same time.