When you choose to have your TurboTax fees deducted from your federal refund, you also pay an additional refund processing fee of $39.99 ($44.99 in CA). If your federal refund is not enough then you cannot choose refund processing. And it will save you money to forgo that anyhow--pay upfront with a credit card and avoid that big fee.
If your TurboTax account fees are $89, there is a Refund Processing Fee of $39.99 to pay the account fees with the federal tax refund.
TurboTax will not allow the use of the Refund Processing Service if the amount to be paid from the refund plus the Refund Processing Fee is within a certain percentage of the federal tax refund. You will have to pay the TurboTax account fees with a credit card, which is going to save you the $39.99 Refund Processing Fee service charge.
When one chooses to pay the TurboTax fees out of the Federal refund, the Federal refund must be large enough to cover the product fees, any sales taxes, and the service fee of 39.99 (44.99 for California) for that payment option.
Are you considering sales tax? What does your $89 in fees you mentioned consist of? You didn't say what products you used.
You will avoid the 39.99 (or 44.99) service fee if you pay upfront with credit/debit card or a prepaid debit card you can buy in a store.