Sorry for the flip flop, after I read the check list again, I thought that you better check the box as not living together. Well, actually you need to answer some questions to yourself first: Are you considering yourself living in Canada in a permanent basis, such as you pay Tax to Canada government in the past years, you have permanent address (rent or own) in Canada, and your ID shows it as well. Based on the info you provided, all the activities aboard of yours are all temporary, such as visiting your wife, before your marriage, took training in US and such, including the four months of temp. staying with your wife. If your conclusion is that you, in fact, is living in Canada in a permanent basis, the safe bet is still on not living together.
My situation is more clear on this, my wife is a Canadian, and she never spent a day in Canada since 2006, my wife doesn't have any type ID issued by Canada government, except her passport, she doesn't even have a bank account there, let along owns or rents a house there. We both live together in US, working and paying tax to US government, owned property in US, raising a family in US in a permanent basis. Now you see the difference?
If you make clear about your own situation, then you will have your answer confidently.
To answer your question:
1. Yes, you definitely can use one evidence for multiple purposes, if that evidence indeed suit for those purposes.
2. I believe the safe bet is not living together, then it is obvious how to check the correct box on the check list
3. And I think you should go with the first option, if you determined that you are actually living in Canada in a permanent basis.
While your situation is kind of tricky that it seemed there is no wrong to choose one or another, I am talking about the safe bet option for your situation. And if it is true that you determined you are living in Canada, then you don't have to include a separate plan to dress your intention to re-settle in Canada.