Partitioning
Which File System?
If you are using a Win98 boot disk, choose to boot without CD-ROM support -you don't need it yet. Then type "FDISK" at the DOS prompt. If you are using Win95B or up, FDISK will ask you a long winded question about enabling large disk support. In skinny, if you answer yes, all partitions you create in this session will be made FAT32, if you answer No, all partitions created will be made FAT16. Use FAT32 whenever possible, especially for larger hard disks, otherwise you are stuck with the 2.1GB limit of FAT16.
If you are using Windows95, and are unsure of which version you have, simply type "VER" at the DOS prompt. A display of "4.10.1995" tells you your Windows is version "A", and cannot support FAT32 (or partition sizes over 2.1GB). A display of "4.10.1111" tells you that your Windows Is Version B. I would strongly suggest that if you are still running Win95A, upgrade to 98. Upgrading to 98 will offer you not only the use of FAT32, but it offers corrected USB support, as well as improved compatibility with newer CPU's (especially the K6-2 and up families).
Do you… Dual Boot?
MUST make the boot partition use the FAT16 file system. Win NT4.0 does not understand FAT32 natively, and Win9x cannot understand NTFS (NT File system) either. Both can, however, understand FAT16. When you start FDISK, if you booted from a Win95B or later boot disk, you will want to answer
NO to the question about enabling large disk support. This tells the system that all volumes created in this session should be made to use FAT16.
If you are planning to dual boot to Windows2000, then you can use the FAT32 file system for the boot partition since Win2K supports it. Partition your hard disk in anyway that you see fit, then shut down the system and reboot. Again, you will want to boot right to the DOS command prompt, and format your new hard disk. You can format the disk from within Windows, but the drive will not be able support long file names after a Windows format until you reboot.
In either case, you also must install Windows9X onto the system first. Win9X is not a multi O/S aware operating system. So if you install it onto a drive that already has another operating system, it will overwrite that O/S boot code and render the other O/S inoperable. Install Win9X first, then you can proceed with the installation of WinNT/2K, Linux, BeOS, FreeBSD or whatever. The basic rule to follow is to install OSes from dumbest to smartest.
Partitioning Considerations
The only thing that you need to be aware of here is that if you have your primary hard disk partitioned already, adding in the new drive is going to change the letter assignments of those partitions. In all cases, primary partitions of physical devices come first. So if your existing hard disk has two partitions that are C and D, your new hard disk is going to be assigned drive letter D, and the second partition of your primary disk will become drive E.
If you are going to be partitioning your second HDD into more than one part, things are going to get even more complicated then. Any extended and logical partitions on the new drive will come after the logicals for the primary master. Primary partitions of physical drives come first, and then come logical partitions, which will get assigned in bus order. Primary master logicals, then primary slave logicals, then secondary master logicals, then secondary slave logicals. Follow?
If your existing drive has partitions, or you are going to create multiple partitions on your new drive, try and name them in a logical sequence so that you can always keep track of what drive letters corresponds to physical drives. Give the partitions logical names, such as making your boot drive name "Boot_Part_X" , or something to that effect.