I am returning to my home country (Canada) for a two month visit in February. I am currently on an ED visa. While there I plan on getting a new passport because my current passport will have less than 6 months validity on it when I return to Thailand. What do I do about the ED visa stamp? How do I get it transferred? Do I have it transferred in Canada? Or do I have to wait to transfer it when I come back to Thailand?

It can never be transferred. You either obtain a new visa or you show both passport on entry to use a valid visa in old passport.

Now if you are talking about an extension of stay rather than a visa that can be transferred after return into the new passport but both passports would have to be shown and re-entry permit used on entry.