QB Issue Resolution:

If you enter the bill and make two payments, one from each sub account

If you are doing a manual recon you just check off both payment entries against the one bank entry

if you are using banking downloads, I can not help since I do not use that, and I am not sure if that one to two matching can be done – I expect someone who does use banking downloads will chime in and say whether it can be done or not.

Resolution for Issue 'How do I pay a bill from two different sub-accounts?' available: Yes (Solved).
Source: Intuit Community forum.

How do I pay a bill from two different sub-accounts?: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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