Yes, you will need to deposit the funds into your HSA, then withdraw them to reimburse yourself for the expenses.
The tax deduction comes when you contribute (deposit) to your HSA. If you do not deposit the money there, you will not be able to claim the deduction. Your HSA provider reports the amount of your contributions to the IRS, so the amount you say you contribute to your HSA on your tax return has to match what your HSA provider reports.
When you deposit the money to your HSA, you need to explicitly tell your provider that the contribution is for tax year 2014. The reason is that you want to make sure that they report the amount of your 2014 contributions to the IRS correctly.
After you've deposited the amount into your HSA, you can withdraw it to reimburse yourself for an eligible medical expense. In order to be eligible, it needs to be an expense that was incurred while you had the HSA in place. If you had your HSA account in place before you paid the expense, no problem. But if you set up the HSA account after you paid for the expense, you might be out of luck.
The distribution (withdrawal) will be a part of tax year 2015, and you'll see this amount included as part of the gross distributions on your 1099-SA form next year.
When I first set up my HSA, I didn't have any extra money to fund the HSA, so I handled it just like you are talking about. I would wait until I had a medical bill, then deposit the amount I needed into my HSA and withdraw it back out to pay the bill.