You must empty the main fluid pipes using filtered pumps in order to output a second fluid from the Reverse Factory.
Here's an image of the save file I was provided to test the fluid output functionality:

The central main line is the "mixed" output, which can only carry one type of fluid at a time. The filtered pumps on each side pull out each unique type of fluid until the main line is completely empty, which then allows a second type of fluid to enter the main line, which will then be filtered out by another pump, etc. repeat
The red cables are probably not required (I think they might only exist to save on power draw?), but the filter part is absolutely required, to keep the different fluid networks isolated from each other. I'll add this to the main page, or maybe the FAQ's, to make this functionality more obvious, since I don't think this sort of setup is ever required in vanilla.