Welcome to SaleHoo, nice to have another Canadian in our forum :)
You either register your business provincially meaning in your currently province or federally meaning Canada-wide. The main advantage of registering federally is that you can do business across the nation and/or protect your company name nationwide.
I'm not too sure about your second question, but I have read on other 3rd party forums that it is possible to have several websites under 1 LLC. It might be best to consult with a professional.
Please feel free to go through our guide on registering a business in Canada - Link hidden: Login to view
Hope this helps :)