2 kinds of 2fa.

Fido key, you must have the key and push a button on it. The computer will request FIDO from the key and it will enter a special mode. It will blink. At that point all buttons are the same, press any button to auth. You can be logged in to the key using either pin and it is the same FIDO key, no need to switch.

TOTP, this is a time based rolling number that needs to be entered. These are per slot on your Yubikey and you'll want to set them up username, password, and TOTP all on the same slot for one account.

How to best use it, my opinion. I use my onlykey for things I have to login to not inside a browser. So my account to unlock my laptop for example. I also use it to log in to my software password manager, don't use LastPass. Then I use my software password manager for all websites and crap where autofill is a thing.

Any account that does TOTP where the user and pass are in my software password manager I put the TOTP for that account in there too.

Now I have fido 2fa and a password you couldn't memorize if you wanted to on my software password manager.

One trick I've done is short press is password and long press is username tab password for things where sometimes the username is there and sometimes it isn't. You can also do long press username short press password for things where you have enter username page reload enter password like bitwarden does for their login flow.