I'd recommend SFTP (with a program like FileZilla or WinSCP) over Diskaid, but Diskaid should work too.
The "root folder" is usually referred to with a single forward slash (i.e., "/") and the subfolders go along the "tree" from left to right (e.g., ringtones are in /System/Library/Audio/UISounds/, so start by looking for System, then Library, then Audio, then UISounds).
I've used DiskAid in the past as well and as recall, I don't think you can access your system files. Here is a program that not a lot of people know about. It's called "91 PC Suite for iPhone" and I've been using it for the past 2 years now, never had any problems accessing or doing anything! You have to be jailbroken to use it though and it is truly AMAZING and it's FREE! I use it because I'm not a huge fan of iTunes at all.