No worries, just add him to whatever you can, and explain it well in your application in terms of how long you've been together, why there is minimal proof of living together in one place (so far). So give a history of what you've been up to, and then something along the lines of "we have now settled in Canada, are leasing an apartment together and have started joining our lives together..." and attach the proof of the joint account, insurance etc...Just be very clear and very detailed, you will be fine!
Honesty is the best policy and they appreciate that.
If it makes you feel better, my husband travelled for 10 years, with no job in that time, so trust me overcoming obstacles is possible. And we were lucky enough to go from start to finish in less than 4 months, despite I'm sure what would be seen as many red flags. We had an interview too...
But we just celebrated his landing as a PR exactly one year ago yesterday.
Our case I'm sure was unique, however we were upfront, honest and explained absolutely everything!!!