You can do both things at the same time. Applying for emmigration to Candana will not affect anything regarding MBA appliation including Visa interview. But it's not so easy to find a job in Canada even you have USA MBA degree due to the poor job prospect.
US visa officer will not know you are applying for CA residency, so they are not in conflict I guess. But the thing you need to keep in mind is that if your CA residency get granted before you finish your program in US, will you move to CA immediately in order to keep your status there in effect?