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>"there isn't anything inherently "powerful" in a cloaked page. It is just like any other page, except that (if everything works!) the cloaked version is seen by robots only. As such, cloaked pages benefit from linkage, site theme, and all the other factors that go into ranking. Cross-linking cloaked pages shouldn't be a problem. If your cloaking system uses a naming scheme, though, just be sure that you keep your names and links straight".
Hope this helps to clarify the question (and apologies for using the word conventions instead of schemes)
Ideally the script should not force you into a naming scheme, it should use the same URL per page delivered regardless of visitor. The script determines what content to show for the requested URL. How the pages are stored on the server is a different matter, but those paths should be internal to the script, a cloaking script should not require you to use those paths to serve up content selectively or to point to other pages with links.
By preserving the URL you can use the exact same link code on the cloaked pages as you would for the real ones. If the script uses a naming scheme, then the SE will index the pages with a URL that will not be what is displayed to a user arriving at your site.