Currently, there is a limitation with the internal flow template, where you can only create one inlet/outlet per capping face. There are a couple of workarounds mentioned below to overcome this limitation:

1. Go ahead with automatic setup through internal flow template. Once the run starts, pause it, display fluid domain and manually change/assign inlet outlets.

2. Create a fluid body manually instead of with the Create Solution button, and you can now pick as many inlet/outlets as you want with the setup tool.