Deposit it all on one account and transfer $50 from that account to the other account.  Or include a -50 line item on the deposit itself using the other account.

Resolution for '50 line item issue: 'Check received for $100 and I want $50 deposited into account A and $50 deposited into account B. How do I do it?' available: Yes.

The 50 line item 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 50 line item issue yourself by looking for a resolution described in the article. If it is a complex 50 line item issue or you are unable to solve the issue, you may contact us by clicking here or by using other 50 line item support options.

For more information about resolving issues related to 50 line item in Quickbooks/QBO or to get support for the issue 'Check received for $100 and I want $50 deposited into account A and $50 deposited into account B. How do I do it?', click the link below: