IS it best to configure permissions within a website for Administration access, separate webPages, or a completely separate application to administer changes on the site?
I usually configure permissions within the same website and have separate web pages for administration.
In some cases, having the same page with more controls can be useful as well, for instance, if you want a page to Approve/Reject comments, or something like that, instead of creating a separate interface you just add a few buttons depending on the role of the logged in user.
I often find that with questions starting "Is it best to" that there's usually a someone and a sometime involved (a kind of pragmatics type thinking - whome and in what context)
Different contexts will offer up different pro's and con's for each of the scenarios you've presented here and depending on who requires what functionality may also sway your choice.
With regard to the "who" part there may be other questions you'll be asking yourself about the process you're going through. Is it my users that require admin access, is it my development team, is it the managing director with little I.T. experience etc etc.
Questions about the medium used may also play a role in the decision you make. Are the "admin" people going to be on a PC, sales reps on-the-road using a palmtop which might suit it's own software application etc.