The quick answer, you're pretty much there. Check value of Current in the key HKEY_LOCAL_MACHINE\SYSTEM\Select. This will tell you which of the CurrentControlSet00X's you need to make your change in.
For example, if Current is set to 2, you need to edit HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet002 with your changes.
The way it works is this:
Windows always keeps a few copies of this key, suffixed 001 to 003 (only 2 in Windows 7 I think?). CurrentControlSet001, CurrentControlSet002 and CurrentControlSet003. Think of them as the master keys that are persistent while the computer is switched off.
When you log into Windows, it picks the last used key, using the value of Current in the HKEY_LOCAL_MACHINE\SYSTEM\Select key. The content is copied into a key called HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet. This key is what Windows plays with while you are logged on.
When you log off of Windows, changes are written back to the key that was original copied from when you first logged on. CurrentControlSet002 for example. CurrentControlSet vanishes, so to speak. This is why you are unable to see it while you are logged off, working from the recovery console :-)
Probably a bit over the top with my answer (I blame the Red Bull), but I figured I'd answer a detailed question with a detailed answer.
Best Answer
I have only done it a few times.
You select HKLM in your current registry, and then the File/Load Hive operation will become usable.
It is a very strange operation to drop in a hive into the registry and edit it, using the quick method, but it worked.
File means you have to find the registry hive file itself by browsing.
Windows\System32\configLoad in and name this "other" hive section which will look like it has become part of your current registry. Use a really obvious and different name, so you can find it.
The strange thing was why I would want to view this all mixed into my current registry, but thats what they said to do ?? There must be a better way to clear the slate and load in ONLY the one hive I want to edit, but it worked, so I rolled with it. I had a full backup, so that helped when presented with this odd method.
Whatever you do certannly do not Import it in, that would be a mess.
Make your changes, which should change it immediatly, Then unload the hive File/Unload Hive and then close. Selecting unload hive unloads the one you loaded (there are no options then).
more info http://technet.microsoft.com/en-us/library/cc732157.aspx although a good tutorial with pictures is what I used the first time.