The withholding in box 4 on the 1099-R (or state withholding in box 12) will be applied to all other W-2 and 1099 withholding on line 17 on the 1040 form (or state form) to be applied to offset any tax liability you have. That will reduce any tax owed or add to any refund.
If you added the amount withheld from other funds so that the entire box 1 amount was rolled over then:
Be sure that when entering the 1099-R that you say that it was rolled over and answer the follow up question that "yes, you added the amount withheld to total the box 1 amount rolled over".
**Disclaimer: This post is for discussion purposes only and is NOT tax advice. The author takes no responsibility for the accuracy of any information in this post.**
