There's only one place it can go if there's only one battery. I'm guessing that this unit will prioritize how much time it sends power to each battery based on that switch. Will that time be wasted on a battery that's not present? Only through testing or by contacting the manufacturer will one find out.
The switches prioritize batteries based on state of charge, not time.
It is clear that if only one battery is connected it gets 100%.
It is not quite clear that if two batteries are connected that the undercharged battery gets 100% of the current when the other battery is full. They say "more" rather than "100%".
I'm probably splitting hairs with that question.
From the manual:
"The SunSaver Duo can charge just 1 battery connected to either the Battery #1 or Battery #2 connections. If Battery #1 or Battery #2 is missing, the remaining battery will be charged with
100% of available power regardless of the charging priority setting."
"The 90% / 10% priority setting allows Battery #1 to receive 90% of available charging current, while Battery #2 receives 10% of charging current. This setting is ideal for RV and boat systems where a “house” bank requires most of the available charge current and a separate engine starter battery requires only a “trickle charge” to remain topped-off. When Battery #1 reaches full charge,
more charge current will be diverted to Battery #2 as needed.
The 50% / 50% priority setting splits available charge current equally between two battery banks. This priority setting is ideal for systems with two equal-sized battery banks that require simultaneous charging. If one battery bank reaches full charge before the other,
more charge current will be diverted to the lower state of-charge battery."