Seperate hard drives and swap racks are what to use. Nearly everyone who dual-boots with a single hard disk (and sometimes with more than one) has this happen sooner or later. The simpler and easier solution is total segregation by using different, swappable drives.
The dual-boot custom evolved when hard drives were expensive and having two would deter potential Linux users. Those days are years ago.
Swap racks are ten-fifteen bucks (I never buy seperate trays since ya don't save much) and extra drives are cheap.
The best answer to questions about dual-booting is similar that to "Doc, it hurts when I do this!"
"Don't do that. "