Due to income restrictions I could not contribute directly to a Roth IRA. I chose to do a backdoor Roth and because of that I am being told I have a 6% penalty each year

Executing and reporting a backdoor Roth IRA conversion as part of your tax return does not generate any penalties.  However, entering information into your return reporting that you made a direct contribution to a Roth IRA when you were not eligible will cause the penalty.  

The backdoor Roth IRA conversion consists of making a non-deductible contribution to a Traditional IRA.  This non-deductible contribution is reported on your tax return.  

Then, the Traditional IRA is converted to a Roth IRA.  The conversion is reported on Form 1099-R, which is included as part of your tax return.  Since the funds being converted were not deductible, the conversion is non-taxable (unless earnings were also converted).

The following TurboTax help article goes through the process of reporting this situation in your return:

How do I enter a backdoor Roth IRA conversion?