That's a good point about the "System Restore" backup point, or whatever they are exactly. With both my wife and my father-in-law, one day their drives were almost full...it turns out System Restore had (literally) ballooned up to over 50GB (!) on their 120GB drives.
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I don't think it matters where the drive is, as long as it is your Mac OS X boot up drive. In other words, you can't have the Mac OS System files on one drive, and then the Windows on another. Both Windows and Mac have to boot from the same drive.
It isn't too hard (at least it didn't used to be) to have the Mac OS System-boot files on one drive, and your home folder on another drive. This would give you space to put your Windows files all on the same 128GB SSD with your Mac OS System boot drive.