Would our time in China be classed as living together? I will of course mention this in the notes but I am not sure if I should select 'yes' as no bills were in my name, everything was of course under her name and I was just in the country as a visitor. My visit visa was good for 90 days where I took day trips to Taiwan in order to 'reset' my visa. (not sure how this may look to UK immigration however Chinese authorities seemed to have no issues with it and I heard of a lot of foreigners doing the same thing in east Asia)
No, you were not living together... as you said, you were only visiting her, while SHE lived there. As you had a visitor visa, you could not legally live with her, because you need a residency visa for that.
So, there's no 'best way to proceed'.. you simply tick NO to the question about living together and move on to the next section of the application.
You can only tick yes to the living together question if you were legally living in the same country as each other on proper visas and you legally lived together, with both your names on tenancy agreements, utility bills etc. (i.e. you both moved to China on 1-year work visas and lived together for that whole year).
The majority of people applying for a spousal visa will have never been able to live together, because they will have always lived in different countries and only visited each other for short periods of time.
Also, when we scan our passports, will each page with entry/exit stamps need to be scanned or just the biodata page?
For you, you only scan the biodata page, because you are only providing it to prove your identity and nationality.
For her, she physically mails her current passport to New York, because the visa has to be put inside it when it is issued. For any previous, expired passports, she should scan every page.