As far as I know, the slipstreamed CD will work like the original one: for clean install, delete the existing partition, create a new one you'll get the option to choose FAT32 or NTFS there. the format is a propertu of the partition, not the of the contents of the CD.

Don't want to slipstream for a clean install at the moment. Just want the ability to run a Repair if needed in order to salvage my stuff. Your statements seem to verify my assumption that my current FAT partition will not cause any problems in the slipstream process so I'll give it a go. Thanks for your input.