Im not exactely sure what you mean
usually, a debug exe will go to bin\debug while a release exe will go to bin\release - all this is customisable in the build settings for a project
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And also, if I am unable to copy and paste the original source files into a new directory, and work on a separate project, how can I keep new versions in separate directories?
ok, what I would do is (depending on why Im doing this)
a) add a new project to my solution, and work on a copy of the files there - note that they are now completly separate from the original files, there's no going back - unless you do a manual process, for that you could use a 'difference' tool - I use 'Beyond Compare' from Scooter Software
OR
b) use source control, and 'branch' my changes, with a view that I might merge the code back into the mainline at some later stage
You havnt provided enough info on why you are doing this
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And also, if I am unable to copy and paste the original source files into a new directory, and work on a separate project, how can I keep new versions in separate directories?
so its a bit hard to advise you further (I'd be leaning towards source control personally... if you dont like command-line stuff, get a (free :-) ) copy of Atlassian SourceTree and use that)