In theory, the pump choices are sensible. Could you provide an exact model number for the lower pump, please? If it's pressure-operated, then I think that could explain its behaviour. If 'flow', then it doesn't make sense to me. Anyhoo - can you answer, please - does the lower pump CONTINUE to run for as long as the upper one is running? I'd also suggest that a good step to take would be to contact ST themselves, and give them a summary of the info as you've given us, complete with diagram.