With a guitar plugged into the FX unit, and then plugging that into the console, you are running everything in series.
But using an AUX send means now the effect is in parallel with the dry signal. If you haven’t already, set the wet/dry control on the FX unit to 100% wet. The extra latency on the dry signal will not mix nicely (unless you’re looking for that kind of effect) with the dry path in the console. You also probably only need to use one AUX to feed the FX unit. I’m not familiar with the M300, but almost all FX units sum the left and right inputs before processing them (there are exceptions, but they are generally not the cheap ones). The resulting effect will be “stereo”, so feel free to use a stereo return, but the stereo inputs are usually just there to preserve the stereo dry signal, which you are now ignoring.
Geoff