Can I switch between my Physical Debit Card and the same card from my Apple Wallet?

So I'm travelling to NYC for the first time and I have some questions about using the OMNY system.

I've created an OMNY account and want to use it to track my progress towards the fare cap. But there seems to be no way to add my Apple Wallet to my account. Apple play uses a diffrent number from what's on the physical card. So if I add my physical card and then use it through Apple Pay, will it still get recognized? And can I kep switching between the physical card and Apple Pay

Also, would it be better if I just used my physical card all the time, if my goal is to track the payments on my OMNY account?

Thank you.