I'm not sure why this issue confuses so many people on a regular basis.

This is what I do:
1) Check in for flight leaving Canada with Canadian passport.
2) When arriving at destination country use second passport for customs and immigration.
3) Check in for flight leaving destination and returning to Canada with Canadian passport.
3a) If departure country has passport check (Most in EU) use second passport
4) Arrive in Canada and fill out e311 and head to Nexus kiosk or CBSA agent and show Canadian passport.

People seem to really worry about not having "the stamps" in their Canadian passport to show where you traveled to. You have no obligation to have "stamps" in your Canadian passport. I have never been questioned about this and frankly it is none of their business.