Filed with turbo tax and paid fees, then was direct deposited after fees removed. How will this effect the stimulus payment going to my direct deposit again?

If your tax return has your personal bank information that was used to either receive a direct deposit of your refund or was used to pay your tax due then the IRS has your bank information to use for your direct deposit of your stimulus check.

To clarify, the IRS has bank information even when the Turbo Tax fee was taken from the refund via the 3rd party, then direct deposited?

Yes, if your tax return has your personal bank information that was used to either receive a direct deposit of your refund or was used to pay your tax due then the IRS has your bank information to use for your direct deposit of your stimulus check.