AS mentioned above, you are trying to show you were NOT common-law before she landed as a PR. There have been others on this forum in identical situations (shared accommodation for work or school but in different rooms), where the visa officer tried to make the claim they were in fact common-law and should have been declared. The applicant/sponsor needed to then prove they were not actually cohabiting due to different rooms. So just make sure you explain clearly in the app you were NOT COHABITING while living there for work and maintained different units in the same appartment.
To apply as conjugal you must have been together for at least 1 year, so sound like you are ok. Please do read the OP manual I linked to above, under all the conjugal sections. This will tell you what proof you must include.
She can apply to sponsor you before she has filed Canadian tax return.