if i took an covid distribution from my 401k but am still making contributions from my paycheck every two weeks, do those contibutions count as paypack and do they reduce my total taxes owed?

No they are not considered a payback.   

You have to make separate after-tax payments to the plan trustee.  You can't just send them checks, there will be a specific form to fill out for the return of a CARES distribution.  And your current pre-tax contributions count as contributions unless you stop them, take the money in your paycheck, and then use it to make separate payments back.