I have looked about every where, except the right place apparently. I am trying to make a selection on a still and make a new layer of it, as in photoshop (ctrl + J) without losing the original. When I make a selection with the pen tool, well you know what happens. Would someone please point me in the right direction? Thank you.
Selections? There is no such thing as selections in AE. Masks are masks and their behavior is analogous to PS' vector masks. If you want to mimic selection behavior, you need to eitehr use the keying tools with additional effects thereafter (Invert, Levels) or such oldschool effects like the Eyedropper Fill, again combined with additional effects (Shift Channels, Levels). That aside - if you just want to mask a specific reagion, duplicating is the correct way to do things. You simply apply no mask to the bottom layer and only cut out the ones above, to which you then apply your effects. If you just need a path for a stroke or similar, simply set the mode of the mask to None instead of the default Add.
Thank you Mylenium, that's the help I was looking for.