I was in a similar situation not too long ago... here's what I did...
Assuming you are using Windows 9X, I would not use DOS to copy your files accross... there are undoubtedly long filenames which will probably get messed up if you do this using DOS...
Anyways, first, configure the drive as a slave, install and FDISK it... If you are making multiple partitions, make sure that the partitions atleast have enough space to hold your files in the correct drives (unless you want to play with Registry entries - which I would advise against)...
After FDISK, you will need to restart the computer...
Then format the drive from with-in Windows, run a scandisk to ensure that there are no faults with the drive.
Then just copy (I used the Windows Explorer) the files from the original drive to the new one... I was able to copy everything, except for the Windows SWAP File (C:\WINDOWS\WIN386.SWP)...
After this, create a boot floppy, and shutdown...
Swap Master and Slave drives over, and boot with your floppy.
Once running in DOS, run FDISK again, and set the Active partition on the new drive, reboot the PC (take the floppy out) and it should boot properly into Windows... Make sure all your files and apps are there and working before you get rid of your old drive...
As always... It is always better to make backups of all the important items on your machine before you do this...
Also, using this method, if there is currently anything on your new slave drive, it will be erased... so back that up as well if you need to...
Hope this helps...
AV