If you are doing everything in the box (not mic'ing a speaker cab and recording that) then you don't need to use the JCR to reamp, you can just reamp using the usb connection (page 86 in the manual and other threads on here tell you how).

If you are using the 11r as a pre/power amp rig and recording the guitar through a mic'ed cab into another non-11r interface (as opposed to recording direct through the 11r USB) use whatever setup instructions came with the JCR.