I need to split the amount between cost of goods and shipping expense

If you are buying inventory items and have QBO plus, inbound shipping, taxes, duties are all part of item cost – per the IRS, and are not posted separately.

If I enter the charged amount as a straight credit […]

Resolution for 'bill comes issue: 'Best way to connect credit card charges to bills' available: Yes.

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

For more information about resolving issues related to bill comes in Quickbooks/QBO or to get support for the issue 'Best way to connect credit card charges to bills', click the link below: