@szliuhff
There is no difference in the procedure and it does not matter which account the excess is removed from. You have to report what you actually did, so you will report a $100 direct contribution in the HSA section, and the $4150 will be captured from your W-2. (You can't just pretend the $100 direct contribution didn't happen, and you can't change your W-2.) Turbotax doesn't ask, know, or care that you have 2 separate accounts, it's not something captured on the tax forms sent to the IRS, the IRS just needs to know the annual total. Turbotax will identify the excess and ask if you will remove it before the April 15 deadline. It doesn't matter which account you remove the excess from, so I would take it from the account that earns less interest, so you have less miscellaneous income to report.
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