QB Issue Resolution:

You can create a Sales Receipt or an Invoice with two line Items each linked to their respective Income Accounts. Enter the amount for each line for the correct allocation. Use the Undeposited Funds Account to hold all the Customer Checks before you ‘Make Deposit’. This will allow you to properly categorize the Income or split the Income on the Check but deposit a single line item for each customer check.

Here are few useful links:

Undeposited Funds: http://support.quickbooks.intuit.com/support/articles/INF12293

Resolution for Issue 'Printing a deposit slip when checks are allocated to two revenue accounts' available: Yes (Solved).
Source: Intuit Community forum.

Printing a deposit slip when checks are allocated to two revenue 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.

Support for Banking
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