I have been making payments to the IRS for owing last year if I still owe will they take what is owed

Yes, they will seize any 2019 tax refund and apply that to the taxes owed.

Thanks. It doesn't show on my transcript that is why I am asking. 

When you file your return with a refund and you have a balance due from a prior year, the information is sent a specific department in the IRS. The IRS system does not automatically apply what is still owing and sends you what is left of your refund. The process requires individuals to be involved in the process. This causes the delay in showing up on your transcript.