The second drive is a separate volume. At a minimum, you will see two volumes (C and D) when you install.
Best option is based on which drive is fastest. If your old drive is a 7200rpm and the new one is a 5400rpm, just add the second drive, boot to DOS, FDISK it, format it, and put your download archives and TEMP directories there. Keep the swap file on your existing drive.
If your new drive is larger and faster than your existing one (has smaller seek rating, same or faster RPM, and bigger cache), which is quite likely, set it up temporarily as the only drive in your system and use a Win98 EBD floppy to FDISK it (pay attention to the cluster sizes as you make a 'Primary' FAT32 partition and make it Active, then allocate remaining space as Extended volume) and format /s it. Then reconfigure it as slave and your original drive as master, and with Windows running:
In Windows Explorer, go into View, Folder Options. Select the advanced options list and disable ALL 'hide files' and 'hide extensions' options if you haven't already done so. You should end up with all files and all extensions visible. If there are any entries concerning 'file indexing service', disable that feature. Apply the settings, then 'Make all folders look like this one' before closing.
In Windows Explorer, select the root files in C: and copy all but io.sys, win386.swp, and command.com (you can also leave any 'bak' files behind) to the root of your new drive's first partition. Next, make a WINDOWS directory on the drive and copy all of C:\Windows directory content to it except the C:\Windows\Temp directory. Make an empty Temp directory in your new Windows directory. (Don't just copy the Windows directory over, we're trying to exclude Temp's contents without leaving a hole.) NOTE: If there is a win386.swp file in Windows, do not attempt to copy it.
Finally, select the remaining directories on the drive and copy that entire lot over, excluding the Recycle Bin and any recognisable spyware directories. Also do not copy virus vaults over.
If any error messages appear, repeat that operation while leaving out the individual file that caused the error.
Finally... Shut down, and reconfigure the new drive as Master and the old as Slave. You should have a faster machine when you reboot. Verify that all your applications are running. When you are satisfied with the transfer, reformat the partition(s) on the second drive.
Note on programs that use 'license files' on disk: After you have copied everything over to the new drive, but before shutting down and swapping them to the new setup, unmount the licenses back to floppy. After swapping the drives, remount the license files (on the new drive, of course) as you test the programs, if they request it to recover the license. At worst case, you recovered the license before the drive swap and put it back in for the new one. At best, you just cloned the license file and the program will work without re-licensing. As you're not planning to spawn these license files to others, consider it a fair backup.
