I live in Montreal but worked virtually for a company that is located in Ontario. I have been taxed in Ontario but not in Quebec. How would i file my taxes?

Are you an employee or are you self-employed (independent contractor)?

I am an employee working for a company

Then you would file normally, just skip entering the Releve 1 if you don't get one.

But I am a resident of quebec, wouldn't I be expected to be taxed in Quebec??

Yes. And as a resident of Quebec, you would normally choose Quebec as your province, and you would pay your income taxes to Quebec. If the amount of taxes you paid on your pay cheques from Ontario are not correct for Quebec, then your income taxes owing/refund will be adjusted to make up the difference.

So are you saying I should just submit it normally and they will notice that I am paying taxes for Ontario and will then switch it to Quebec and I just pay any difference for it?

Yes. That's part of the reason you submit an income tax return even though you've already paid income tax on your pay cheques, to fix issues like this. 

I am in the same situation and am confused about how TurboTax is entering amounts/data when I skip the RL1: https://turbotax.community.intuit.ca/community/quebec-taxes/discussion/how-to-enter-t4-without-rl1-skipping-the-rl1-still-inputs-data/01/3332643

Yes, it is transferred correctly. Further along in the Provincial section of your return- Your Other Québec Credits Profile - you will check off the box  "Tax transfer for residents of Québec who earned income in another province and from which federal tax was deducted" Continue- Tax Transfer for Residents of Québec- on this page you will enter Income tax deducted by employers outside Québec. This step is crucial so that you don't end up with a big refund on the federal side and owe a lot on the Provincial side.

Thank you for choosing TurboTax.

I'm in the same situation - living in Quebec, worked for an Ontario company virtually. I entered my new address, and filled out my T4, but I haven't been prompted for any Quebec-related credits or even to fill out an RL-1. The section you mentioned "Your Other Quebec Credits Profile" hasn't appeared and isn't an option in the search bar. Is there something I'm missing?

@aluckwman 

Did you select Quebec as your province? When you click on Tax Home on the left side menu, and then click on the Provincial button, do you see Quebec related items listed there (ex: "Other Quebec Credits")?

Thank you so much, this worked!