Yes, there is a 2 step process to reporting a backdoor Roth. First, it sounds like you may have reported the contribution as a direct Roth contribution, resulting in the "income above the limit" issue. Since you did not contribute directly to a Roth, you need to indicate you made a traditional IRA contribution. If your income is too high for a traditional IRA, it is automatically non-deductible, otherwise, you check the box to make it optionally nondeductible.
Next, when you enter the 1099-R, you need to indicate that the money was converted to a Roth. Answer the questions that follow the 1099-R entry, until you reach Tell us if you moved the money through a rollover or conversion. Select I converted some or all of it to a Roth IRA and Continue.
Next, select Yes, all of this money was converted to a Roth IRA.
For more information, see: How do I enter a backdoor Roth IRA conversion?
