Scheduled Automatic Deductions

"Correctly" is probably not the "correct" term; but I don't think you understand the alternative correctly.

I assume you're talking about your medicare insurance premiums, which are the same each month (until a new year rolls around).

You can set that up as a Scheduled Transaction to be entered into your checking account register "automatically" by Quicken, on, or before, the day the actual transaction will clear your bank. Then when you download the actual transaction, it will "Match" the transaction already in your Quicken register and not create a new transaction when you Accept it.

If the amount being deducted from your checking account differed each month, the change you should make to the above procedure would be to have Quicken "remind" you to Enter the transaction. Then when the actual transaction has cleared the bank, and you see it in the "Accept transactions into register" window in Quicken ... you would: note the amount, switch to the "Scheduled Bills & Deposits" tab at the foot of your register, select the Scheduled Transaction, click "Enter", modify the amount to agree with the downloaded amount, and Enter the scheduled transaction. Then switch back to the "Downloaded Transactions" tab, where you would see that the downloaded transaction status had changed from "New" to "Match" and you could Accept the transaction.

At no time in this process would you be sending anything to your bank, nor would any check number be required. When you setup the Scheduled Transaction, you tell Quicken the payment "Method" is "Payment"; NOT "Printed Check" and NOT "Online Payment from Quicken" ... thus nothing is transmitted to your bank and no check number is involved.