Synchronize with 2-factor ID

Quicken only uses Direct Connect for brokerage accounts.
Direct Connect has a different security model than the website.  So most likely if you turn on 2-factor identification on their website it will have no effect on you downloading transactions.

I don't know of any financial institution where multiple factor identification affects Direct Connect, but if it was to happen, and if Quicken understands how to handle it, Quicken would prompt you.  There isn't any way to "setup/sync" such information.