Most modern systems don't really need the Master/Slave configuration configured properly, just not to have both drives set to the same setting. Your BIOS boot order will override the master/slave boot setting (Dells are an exception, they're picky about this).
Windows XP and vista are picky about hardware, 98 or 2000 will boot on just about anything. Just a couple weeks ago I took a win2k hard drive out of an Athlon XP and put it into an Atlon 64 X2 system and it worked fine (lousy screen resolution because it needed video drivers installed, but it worked). But it doesn't sound like you want it to boot.
Formatting is never a bad idea when adding a new drive, but you can just erase the data you don't want and use the file system as is. I would, however, discourage this if it's Windows 98. You want an NTFS file system and WIN98 used FAT32.