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Your other computers shouldn't be affected by you dual booting.
I take it the the 6.8GB HDD is going to house XP and the 2.3GB HDD is going to house 98SE?
Keep in mind, in order to do it that way, C: will HAVE to be FAT32, 98SE has to put some files on the C: drive in order to boot. Your setup is actually a good idea, especially if you're not going to be using 98SE that much. No sense on putting it in the first part of the drive, put the one your going to use the most so it will be faster.
Also keep in mind, you'll have to install 98 first, then XP. XP will recognize that you have 98SE and will add it to the boot loader so you can choose between the two during boot up.
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