Accounts now only give me the option for check pay

If your bank (the one that runs your checking account) recently required you to reauthorize your checking account and/or your bank has changed from "Direct Connect" to either "Express Web Connect" or "Express Web Connect+" you can no longer use Online Bill Pay direct to the bank or Quicken Bill Manager's Quick Pay function. The bank no longer supports this function through Quicken.

IMHO, you have these alternatives (in no particular order of preference):

1. Use Quicken Bill Manager's Check Pay making sure to submit payment early enough (at least 3 weeks before due date) to allow time for delivery and processing. Note: limited number of free transactions per month.
2. Logon to the bank's website and schedule your bill pay payments to be executed by the bank from your checking account. In parallel to that, in Quicken use a regular Scheduled Reminder to record your payment. Repeat both actions every time another payment is due.
3. Bypass Bill Manager. Let the biller's computer system do all the work for you. Logon to the biller's website once and set up their Autopay, APS, Direct debit, etc. service to make the current payment and all future payments on Due Date directly from your checking account. In parallel to that, in Quicken, every month, record a regular Scheduled Reminder to keep track of your payments before they come due.
4. Write (or print with Quicken) a paper check and mail it to the biller, making sure to mail payment early enough (at least 10 days before due date) to allow time for delivery and processing.

I've been using method #3 for decades, since before the Internet and bank download capabilities were even introduced. It's easy to get used to this process. And I have yet to miss a single payment.

Which means that you are using the process I describe in #3. You can still use Bill Manager to retrieve the monthly statement, but you should not link the online bill to the scheduled reminder.
Record the (now offline) reminder when you receive notice of the new statement and its amount.
When you download transactions after the due date, the downloaded autopay will match to the already existing register transaction and all will be fine.