You are asking two different things here, but yes, you can run the 11R into the fx loop of your amp. You can also run the 11R into the guitar input of your amp. It really depends on how you want to use it. The Output to amp connections are instrument level and work well going into the guitar input of your amp. This way you can use the stomps in front of your amp.
Running it in the fox loop will allow you to use it as an fx processor while using your amps tones.
You can also just plug the 11R into just the fx return of your amp if you want to use the amp modeling and fx in the 11R and power amp and speaker of your amp.
There are many ways to set it up. Have a look through the
11R Manual for more info and enjoy.