Thank you for that question, it clearly needs to be clarified in the new framework.
1. Start with your primitive structure in the Builder. Give it an obvious name, like "GaAs primitive"
2. Still in the Builder, create the supercell, e.g. by repetition and randomization etc. Name it accordingly, like "InGaAs supercell"
3. Send the supercell to the Workflow Builder
4. Insert a calculator block and the Effective Band Structure block
5. As you see now, there is a warning (error, really) that the primitive configuration is missing
6. Insert a "Configuration(s)" block
7. Move it to the top of the script
8. Open "Configuration(s)" block (double-click), and click the +. By default, this let's you add structures from the Builder stash file. Pick the primitive structure.
9. Optional: drag the inserted configuration out of the Configurations block, and above it. Then you can delete the Configuration(s) container
10. Optional, but nice for clarity: Select each configuration block, press F2 and rename them "supercell" and "primitive" respectively. Now you can easily check that the primitive cell is assigned to the corresponding keyword in the EffectiveBandstructure call in the script
Not entirely obvious without guidance, I agree, but you can now save the workflow and reuse it for many different structures.