I have 1099R and a 5498 for the same amount but I cannot get the 5498 to offset the 1099R. What am I doing wrong?

You should only enter the amount that is on the form 1099-R.  The Form 5498 is for informational purposes only and is not reported on your income tax return. If you have made any deductible contributions to IRA account(s), you would first enter the form 1099-R in the income section and answer follow up questions.  Then, you would visit Deductions and Credits and enter your contributions to lower/offset your Adjusted Gross Income. 

To enter 1099-R:

1. Federal Taxes
2. Wages and Income
3. Scroll down to Retirement Plans and Social Security
4. Select IRA, 401(k), Pension Plans (1099-R)

To enter IRA contributions:

1. Federal Taxes   
2. Deductions & Credits (you may have to select See all tax breaks)
3. Scroll down to Retirements and Investments
4. Select Traditional and Roth IRA Contributions