CMS Site Structures

I am currently re-developing my home grown ASP.Net based CMS 
application and am debating changing the way that I structure the admin 
system.

In the past I have used two sites, one for displaying the content and 
then another using a different URL for the content administration, 
however there are some drawback relating the file uploading/handling.

I am now considering moving the administration site into a sub 
directory of the main site, which will get over some of the drawbacks, 
but could present other issues.

How do most other CMS applications structure their sites.


Any pointers or views would be appreciate.

Cheers,

Julian Voelcker