Drive 1 -- Mac backup. I prefer and recommend either CarbonCopyCloner or SuperDuper to create bootable cloned backups. I DO NOT recommend Time Machine, ever.
Drive 2 -- Windows backup. I don't use bootcamp nor do I have Windows installed to "boot natively". But if you do, I've heard that there's something called "WinClone" that can clone a Windows installation to a backup drive. That's what I'd suggest.
I -WOULD NOT- recommend keeping both backups on one drive.
For Windows you'll likely need to use NTFS for your backup drive. For Mac you'll definitely need HFS+ or AFPS for Time Machine.
While there is software drivers you can install that allows Windows to read and write HFS+ and Mac to read and write NTFS, you cannot use the default backup applications to backup to these drives, only third party software.
That said I have a NAS setup that my MacBook Pro and my Surface Pro both can backup to the same drive, and the drive is formatted Ext3…