I owe the irs money from 2014. Been making payment arrangements. I owe them about 400. Im getting over 1000 this year. After they pull whats owed do i get the rest still?

Yes, if the IRS garnish your refund for back yax, they will refund you any balance remaining.

I filled on april 3 or 4th. So will it take longer to receive it? Irs website says 21 days after filling to recieve a refund.

It may take longer if the IRS garnishes your refund.