Retirement tax questions

You can leave the zero, but also check the box in the interview that you rolled the funds over.  After entering the 1099-R, continue through the interview. You'll be asked "Did you roll over all of this $xx (Box 1) to another retirement account?", select "Yes, I rolled over $xx to another traditional IRA or retirement account (or returned it to the same account." Note- you may need to check the "taxable amount not determined" box in the 1099-R entry if this option doesn't appear to you in the interview.