Funny, I've just had to deal with the same thing :)

Sounds like you're on your own here, so why not do what I'm doing?

Mirror the install on your desktop, and move code over only when thoroughly tested. I use scp:

scp -r /home/userdir user@host.com:/home/
[download]

I'm using Mandrake as the Desktop, but installing and compiling Apache with SSL and mod_perl in the same way I am on the server (rather than using the Mandrake versions), and running the site under the same username with the same directory structure and httpd.conf (excluding the domain, of course, which is set to localhost!), startup.pl and Perl Modules.

Fingers crossed, I haven't encountered any major differences yet. Of course, if you're writing Apache modules, there might be issues, but that's not something I know how to do at the moment, so I can't really comment.

To be honest, I haven't even bothered to see what *nix the server is actually running - I was just dumped on the box and told to get it up and running, and that seemed like the easiest route.

.02

cLive ;-)