The System Reserved partition is a Poor Man's equivalent of a true system volume. It is where Microsoft's Boot Manager and the BCD live. If you have a System Reserved partition then you actually already have a boot manager; and that boot manager is what is currently starting Windows on your system.
By copying around the Windows 7 boot volume, you are just copying around the Windows operating system files and ancillaries, and your applications programs and user data (if they are on the boot volume). If you don't touch the contents of your (Poor Man's) system volume at all, then you won't alter your boot manager.
If you create a duplicate boot volume, then you'll need to tell the boot manager about it, with a new entry for the boot menu. Similarly, if you move a boot partition that's already on the boot menu to a different location, you'll have to tell the boot manager about the new location. Both of these actions involve editing the BCD database with the
BCDEdit tool that comes with Windows.