No Problem Highland! The registry is a bit confusing. That's why you always see HUGE WARNINGS about backing it up whenever someone suggest a change in the registry. Anyway...
It isn't a duplicate. It is the actual file. You are just looking at the file through a registry editor. It's kind of like a Word document. When you open a Word document using Microsoft WORD, and make changes, your making changes directly to the Word document. Well when you open the registry editor, you are actually opening the NTUSER.dat file. The only difference is that when you open the registry editor, you are looking at several different NTUSER.dat files, and some other types of system files as well. For example the HKey_Local_Machine Key is actually the "System" file located in WINNT\System32\Config.
To your second question, you always know whose user key your looking at. When you look at HKCU in regedit, it is always the key of the user who is logged on that machine at that time. Now when you are talking about Terminal Server and several users are logged on at the same time, then this is the best way to explain it...
3 users logon to a Terminal Server (User1, User2, and User3). They all open regedit. When User1 looks at HKCU, he is actually looking at NTUSER.dat for User1. When User2 looks at HKCU, he is actually looking at NTUSER.dat for User2. And the same thing goes for User3. So if 50 people run the registry editor on a Terminal Server then they all see a different HKCU, because each user is looking at his/her own NTUSER.dat.
Here is a Microsoft website that describes the functionality of the registry that should help more.
Choose
"Windows 2000 Registry Reference" in the TOC
Dave Namou, MCSE CCEA