You said you got two checks from your employer so that would explain why you got two of the reporting forms. The Form 1099-R is for a pension distribution so that may be unrelated to the other two checks. If it has $0 in box two though, it won't show as taxable on your tax return, so can enter that in the pension income section.
The W-2 sounds right as you said one of the checks was taxable. If the amount on the Form 1099-MISC is not taxable, the company can still feel compelled to report it, as it is not up to them to determine it's taxability. If you know it is not taxable, you can enter it in the 1099-MISC section in TurboTax, then enter a negative adjustment to income to cancel it out. Here is how you can do that:
1. From the Federal menu in TurboTax find Wages and Income
2. Find Less Common Income
3. Choose Miscellaneous Income, 1099-A, 1099-C
4. Choose Other Reportable Income
5. Enter a description for the reduction of income and the adjustment amount as a negative number
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