If I used my HSA money to pay myself back, does this count as a Yes, I used my HSA, or No, I did not use my HSA?

Yes, if you purchased qualified medical expenses then requested a withdrawal from your HSA to cover the expenses, you would indicate that you used the HSA funds so they are not taxed.  I would advise you to keep records of what you purchased and the receipts just in case you need to prove it in the future, but it is perfectly acceptable.

Thank you! So then it asked if I’m going to take out the money by a certain time or i will get taxed 6% on what’s in there now. ??

@joe884 This question is referring to an excess contribution.  You will want to go to the HSA section:

• Answer the questions until you get to the Let's enter your HSA contributions screen.
• Make sure you didn't accidentally re-enter the amount already listed (from box 12 of your W-2) as this will incorrectly double your total contribution amount.
• Continue through the HSA screens, making sure you answered all questions correctly. (make sure you indicated if you had an HDHP)

If you did overfund the HSA, you will need to make a corrective distribution or adjust you 2025 contributions to avoid the 6% penalty.  

See Why am I showing an excess HSA contribution?