Where are your applications in this example? They are on the second hard drive in the application partition. How does Win98 know where they are? It uses the Registry and Shortcuts and other pointers in the c: partition to access these application programs on the e: drive.
The first thing we need to do now that we have installed WinMe on the hard drive is to test out all of our applications to make sure they work properly under WinMe. How is WinMe going to know that our applications are located on drive e:? It knows where these applications are because we copied the Registry and Shortcuts and other pointers from Win98 when we copied the entire partition into the empty partition. WinMe takes advantage of these pointers when it was installed on top of the copy. Now we can use our applications in the e: drive from either Win98 or WinMe. We need to test out all of our applications to make sure they still work under WinMe. If they do not work under WinMe, we can always switch back to Win98 to run them until we can get the latest version that works under WinMe installed on our computer. When all of our applications work, then we can simply delete our Win98 partition and only use WinMe. This is a much safer way to migrate to WinMe.