My ex left the house on october 15, 2018...we changed the marital status through cra in January. how would we file income tax, seprated or married?

You should file your 2018 tax return as "Separated" as you were on December 31st. Be sure you both file your returns with the same date of separation - October 15th, 2018.

Although you must wait 90 days to report your separation to CRA to adjust your benefit amounts (which they will back pay to), on your income tax return you need to report the actual date your Marital Status changed.