When entering medical expenses for the deduction, do I include total paid for the tax year, including out of pocket expenses paid by my HSA account? The last question in the step by step is did you use your HSA disbursement for these medical expenses?

Yes, you will include expenses you paid with your HSA account and then enter the amount when asked that you used of your HSA to pay for the medical expenses.  The HSA is deducted from your total expenses on line 13b of the medical expense worksheet.

Turbotax assumes you are dumb, and don't know that expenses reimbursed by an HSA are not deductible, so it will automatically subtract your HSA from any expenses you list.  So you need to list all your expenses, no matter how they were paid, and let the program do the math for you.