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Yes, the overtime exemption from OBBA is included with the W-2 entry screen. How you enter this depends on the version of TurboTax you are using.    In TurboTax Online, choose "Overtime" from the Category dropdown list for W-2 Box 14. If you don't see this dropdown, follow these steps: After you have entered all your W-2 information, you will come to a screen that says, "Review your box 14 info."  On this page, choose the first option for "Overtime" from the Category dropdown list (if not already selected for you). Continue to the page “Deduct up to $12,500 of your overtime” and hit Continue. Follow the prompts to confirm and/or enter your eligible overtime premium pay and confirm you are not an exempt employee. In TurboTax Desktop: After you have entered all your W-2 information, you will come to a screen that says, "Box 14 is missing info."  On this page, choose the last option for "Other (not classified)" from the Category dropdown list. Continue to the page “Let’s check for uncommon situations” and check the top box for “Overtime.” Continue to the page “Deduct up to $12,500 of your overtime” and hit Continue. TurboTax will ask you if you need help in calculating eligible over time or if you know what to enter. If you know what to enter, and you are not an exempt employee, you will then enter the amount of overtime that is eligible to be deducted on the page “Enter your deductible overtime…”

Did you withdraw the money from your HSA a/c and put it into a non-HSA account? Then it's taxable even if used to pay medical bills. Otherwise, we need more details of what you did and general description of what you did in Turbotax. If you rolled the money from one HSA to another, there will be no entry for it in TurboTax. You still need to enter the Medical expenses paid  

If the EIN is the same and you work in more than 1 state or city, sometimes they will give you another W2 with the extra state information on it and the top part the same or not filled in. If this is the case, enter 1 W-2 but include both state and local taxes on it. It will let you type in more than one line for boxes 15-20. Don’t add the boxes together. If the locality in box 20 is the same you can simply combine the values in boxes 18 and then the values in box 19 together.   Same for boxes 12 and 14 if there is no room on the first W2 they can give you another W2 with the extra boxes on it. So list them all on 1 W2. For box 12 just enter it in the next row or box. It doesn’t have to match the box 12 a-d etc.

It is automatic based on your age.    It is not part of your Standard Deduction. The new Senior Deduction is separate and in addition to the Standard Deduction or your Itemized Deductions on 1040 line 12e. The 6,000/12,000 senior deduction will be calculated on 1040 Schedule 1-A page 2 Part V Enhanced Deduction for Seniors which goes to 1040 line 13b. Turbo Tax automatically includes it if you qualify. For Online version you can preview the 1040 https://ttlc.intuit.com/community/accessing/help/how-do-i-preview-my-turbotax-online-return-before-filing/00/26160 The maximum deduction is $6,000 for each person 65+. The phaseout is 6% of the amount by which MAGI exceeds $75,000 for single or $150,000 for married filing jointly (MFJ). The MAGI is normally the same as your AGI on 1040 line 11 but with some Foreign items from Form 2555 added back in. On a joint return the phaseout is calculated separately for each person, so the 6% phases out for each spouse. You can not get it if you file MFS Married filing Separate.

2025 STANDARD DEDUCTION AMOUNTS SINGLE $15,750  (65 or older/legally blind + $2000) MARRIED FILING SEPARATELY $15,750  (65 or older/legally blind +1600) MARRIED FILING JOINTLY $31,500  (65 or older/legally blind + $1600) HEAD OF HOUSEHOLD $23,625 (65 or older/legally blind + $2000)     For 2025 through 2028 there is an extra  deduction amount of up to $6000 per individual 65 or older filing Single, MFJ, or HOH which is phased out for taxpayers with modified adjusted gross income over $75,000 for single filers and $150,000 for joint filers.   The $6,000 senior deduction will be calculated on 1040 Schedule 1-A page 2 Part V Enhanced Deduction for Seniors which goes to 1040 line 13b. It is separate and in addition to the Standard Deduction or your Itemized Deductions on 1040 line 12e.  Turbo Tax automatically includes it. IRS Schedule 1-A https://www.irs.gov/pub/irs-dft/f1040s1a--dft.pdf  

Where I live, most of that stuff now needs to be ordered directly from irs.gov.  Happily they are good with filling our the orders and ship at no cost.  Funny you should mention doing it manually.  Been there, too.  In fact, I think I might order the forms this year to see if I could fill them out and arrive at the same outcome as Turbo Tax!