You don't enter the 5498. Just enter the 1099R. If you had taxes withheld did you add them back in when you returned the funds?
Enter a 1099R under
Federal Taxes on left
Wages & Income at the top
Then scroll way down to Retirement Plans and Social Security
Then IRA, 401(k), Pension Plans (1099R) – Click Start
If you are filing a Joint return be sure to pick which person it is for.
It's just as fast and easier to manually enter your W2 or 1099. Don't type the bank name or try to import it.
At the bottom pick - Change How I enter my Form
Then on the next screen pick - I'll Type it in Myself
