I opened a Trad IRA, converted to Roth, then removed the entire amount all in 2016. My income is above the IRA limit.

1) Enter the $6,500 Traditional IRA contribution and mark it non-deductible.

Enter IRA contributions here:
Federal Taxes,
Deductions & Credits,
I’ll choose what I work on (if that screen comes up),
Retirement & Investments,
Traditional & Roth IRA contribution.

OR  Use the "Tools" menu  (if online version under My Account) and then "Search Topics" for "ira contributions" which will take you to the same place.

2) Enter the 1099-R for the Traditional IRA to Roth conversion.

Federal Taxes,
Wages & Income
I’ll choose what I work on (if that screen comes up),
Retirement Plans & Social Security,
IRA, 401(k), Pension Plan Withdrawals (1099-R).

OR  Use the "Tools" menu (if online version under My Account) and then "Search Topics" for "1099-R" which will take you to the same place.

Be sure to choose which spouse the 1099-R is for if this is a joint tax return.
Be sure to pick the correct 1099-R type: Standard 1099-R, CSA-1099-R, CSF-1099-R, RRB-1099-R.

When is asks what you did with the money - you moved it to another account.  Then the next screen - you converted it to a Roth.

You will be asked if you tracked your non-deductible basis in the Traditional IRA - say yes, but do not enter an amount for the 2016 contribution, only prior year basis if any.  

Your Traditional IRA to Roth conversion will only be non-taxable if the year end value of all Traditional IRA accounts that you might have is zero - enter the 2016 year end value (hopefully it is zero).

When done,the $6,500 contribution should be taxable on line 15a on the 1040 form and nothing on 15b.

Don't worry about the income summary screen as it will show the total of both distributions - taxable or not.