Hopefully you will take this as me being thorough and not insulting. When the 1/4 valve is "in line" with the pipe, it is open letting fluid go by. When the 1/4 turn valve is perpendicular to pipe it is closed stopping the fluid.
The blue line going in your hot water heater (HWH) is cold water going in and the red line is hot water out to trailer faucets. Those valves should be open when you are using your camper and the line that goes between the red and blue(bypass valve) should be closed. When you winterize, the bypass valve is open and the red and blue valves are closed. This will bypass your HWH and use less rv antifreeze.
The clear lines take water from clean water tank, to the pump and then goes to trailer faucets. The clear lines should be open during normal usage. There probably is a clear short short line that is not hooked into anything with a 1/4 turn on it that comes out of pump. This short line is to pump RV antifreeze throughout trailer and valve should be closed during normal useage. When you want to pump RV antifreeze to winterize, you shut the lines from your tank and open the short line that you put into the gallon of anti freeze.
In short, during normal usage, all water lines should be open position except for bypass on HWH and on the "short" line on water pump. That is how my set up is. Hope this helps.
2012 F350 Lariat CC SRW 6.7L Powerstroke