Ok ... I think you are confused ... did you not get the credit in advance ? So you applied for the credit on the return ? If so then the credit on the return is used to first pay off any taxes on the return and then if there is anything left over it is refunded to you ... none of this goes to an employer at anytime.
Now if there is an understanding with your employer where they will pay the taxes you owe on the return then you need to ask them if that is before any payments or credits happen on the return. I assume you normally don't have any payments/refundable credits on a return however this is not a normal tax year in any way. This is a discussion you need to have with them not us on this forum.
