I use QMac Premier version
I can think of a few ways to do it, here's mine.
First I created a brokerage account named Treasury Direct to hold the I bonds. Then I created a custom security (in the Securities window) for the bond. I put the maturity date in the name - "I-Bond 04/2052" - so if I buy more I Bonds in the future I can track each one separately. I initially priced it at $1 per share, and recorded a purchase of 10,000 shares (for a $10K bond) in the Treasury Direct account. Since the money for the purchase came from my savings account I also entered a transfer of $10K from that account to the Treasury Direct account.
Each month when the bond accrues more interest, I update the price of the bond in the Securities window to match the value of the bond. Currently my bond is worth $10,520, so the price is now $1.052 per share. I don't think there's any automatic price updating available for I Bonds, so it has to be done manually by you.
But if you update the price, then doesn't that show a negative cash balance in the account?
No, because I'm not recording the interest as a separate interest transaction, I'm showing it as an increase in the value of the bond. If the price of a stock goes up, it doesn't affect the cash balance of the brokerage account; this is the same thing.