QB Issue Resolution:

Ok, answering my own question here. When I logged in and navigated to the next screen it provides a drop down selection to choose the company to import into.

Resolution for Issue 'How will the Export to Quickbooks Online know which company to import into if multiple accounts are tied to the email address?' available: Yes (Solved).
Source: Intuit Community forum.

How will the Export to Quickbooks Online know which company to import into if multiple accounts are tied to the email address?: 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 Company
Quickbooks Repair Pro will resolve it efficiently and affordably. Guaranteed resolution of your issue, or you pay nothing!

Error Recovery for Company [Canada]
E-Tech is the #1 Quickbooks data migration and Conversion service provider.

Get 50% off Quickbooks Online

Click Here for 50% off!

Additional Support Options: