you have to look at each province's requirements and procedures individually. some pick from EE pool and send EOI and some require direct applications.
No, just register and apply on their website, you will be required to enter your ee profile number I guess. That's how they tie your ee profile with nomination.
You are not a PR as you did not land yet. You should have informed cic of your marriage immediately after marriage. Your Visa is void now. You need to inform them and get a new visa for you and your wife.