Tech Question with dual boot

[farmerted]

I have an older computer running Windows 98.

This PC has 2 seperate hard drives

HD1 is C: a 20 gig Western Digital in FAT32
HD2 is D: a 40 gig Western Digital also in FAT32

Windows 98 is installed in default c:/Windows

HD2 is my storage space for games and such.

I want to install Windows 2000 professional onto HD2 my D: drive and have the PC dual boot into either 98 or 2000.

It has been a long time since I have done something like this so I am a little rusty. Will 2000 create the boot.ini file automatically for the dual boot or will I need to do this myself?

Also,

Previously I had both 98 and 2000 installed on this same PC but in different partitions on the same hard drive C:

Because of this a boot.ini already exists. I ended up deleting the partition with 2000 and editing the present boot.ini file to autoload 98 after 3 seconds.

Will having the previous boot.ini file cause problems with the new install of 2000 as it will be placed on a seperate physical hard drive this time?

Will it overwrite the present boot.ini file to allow the dual boot of 98 and 2000?

And as 2000 is based on NT will it try to change my format on my D: drive to NTFS instead of using the FAT32 format?

Thanks in advance,