XP Pro 2HD & 3 Master Boots

I have a Gateway 766mhz that came with Windows 98se. I earlier installed a 40g HD which is still FAT32. The second HD has 20g and apparently boots from the 40g HD because I made the mistake of removing one of the HD's when I was installing for some reason which currently escapes me. I know there are 3 master boot sections and I suspect one one the 20g and one on the 40g are win98 leaving the one on the 40g a booted from the 40g (scussi placement "0") I want to remove the Win98 master boots and boot only from the 40g HD, and use the 20 gig to use as a second boot select. I guess my question is am I going to do this with the 7 floppies I formated for XP Pro? Is there anyone out there with enough experience to direct me to the safe place to get help should I need it? Any suggestions? I also have a slipstreamed copy of XP Pro which I put together as a backup on my 40g HD. I can't seem to get it moved to my Maxtor 160g backup HD because of the size and the USB is 1.0 not to mention the error problems I get when I do try to move it which is another question altogether. XP Pro currently works on the 20 g HD (NTFS reformated). and I tried to install XP Pro on the 40g but it wouldn't take even though I tried to reformat ntfs and reinstalled Win98se with the intention of deleting it with the fresh install of XP Pro.
Thanks for reading in advance and if you think you can answer only part of this question please do.

Thanks!

 

I read your post three times, and I'm not sure that I fully understand. If I'm correct, and you only have 2 hard drives, a 20 gig. and a 40 gig. , then there shouldn't be much of a problem. Also Win98 will not install on a NTFS formatted hard drive.

A Win98 bootdisk will fix most of your problems if you are familiar with FDISK and DOS commands. If you don't have a Win98 boot disk, you can download one from bootdisk.com. Start your computer with the floppy disk inserted, let it load, and when finished , type fidisk (?) - whichever drive that you are wanting to reformat. It should give you several options, but the one that you want to use is the one to delete the non dos format partition. Follow the instructions, and when FDISK is finished, reboot your computer with the floppy disk still in the drive. When the reboot is completed, you should be able to type format (?)- the drive that you are working on, and you will have a newly reformatted hard drive without an operating system. The (?) above is meant to be the drive letter of the drive that you are working on , and not taken literally.

I hope this helps, and if I'm wrong, I'm sure that a more experienced member will jump in and correct me.