Do I still make a payment in my second tax return when I already paid a high amount in my first return?

If you owed on the first tax return you made an error on and have already paid more than you feel you should have and then made adjustments to your return, once you have Refiled it you will wait for your updated Notice of Assessment from CRA to advise you if you still owe or not. 

You can contact CRA if you need more information.