It will work fine.
Just use your Win9x startup disk with CD-ROM support.
Do not sys the drive using the 9x disk or you'll get a DOS version conflict error, but you can use it to boot, format, and run the install from the CD or copy the cabs to the HD and run setup from there.
AFAIK the ME disk is bootable. (mine is, and it's the el-cheapo update one).