Yes you can run both at the same time with no problems.  It will boot from which ever one is set as the primary boot device in the bios and the other will be just storage.

They both can be set as master as they are on different hook ups and you will not be able to copy everything on the boot drive only from the other one as the boot drive will have windows files in use and won't copy.  I would boot it and then copy the other drive to you TB drive and then change the boot order and boot from the other one and complete the process.