External pedal effects can physically be placed anywhere in the signal flow, really. The limitation would be the number of physical patch cables you have available to use.

You could put a pedal in between your instrument and the input to the M13. You could put some pedals between the Effect Send of the M13 and the Amp's input jack. You could put an effect in the Amp's Effect Send output into the Effects Return of the M13. And lastly, effects could go in between the Out of the M13 back to the Amp's Effect Return jack. The quality of how your effected signal sounds to you, however is going to be subjective and subject to the interaction of all these hypothetical devices on your sound. You'll definitely have to experiment to find what works best for you.