Just to let you know, you could add your Canadian passport to your GE account at an enrolment centre, then just leave your Canadian passport in the APIS (doesn't really matter if its in the APIS when flying to the UK). I am also a Dual UK/CAN Citizen and added my CAN passport to GE after I got GE on my UK passport (Didn't have a Canadian passport at the time). You can then use both passports on the kiosks.

Also if your planning on being in Canada, apply for the Nexus, its cheaper and makes things even easier.