Cannot drain water separator, sucks air in instead

DFO,do your tanks suck air when you unscrew the cap?

 

If that is your filter pictured, crack it loose from the mount to allow air in the top when water/fuel runs out the bottom. (I'm hoping the picture is just displayed sideways and that's not the way the filter is mounted). Don't worry about the air, the Cummins has a good fuel pump that will fill the filter back up.
Just cycle the key on and leave it on for a minute before starting.

 

Opening the caps won't help.

 

I cannot tell by the photo, but in relation to the fuel tanks and engine, how high is that mounted? If that is the high point in the system then it needs to be relocated lower to prevent gravity from sending the fuel back to the tank, or install a fuel shut off between he filter and tanks.

 

Fuel won't run back to the tank. They install check valves for that. The air rushing in is just equalizing the fuel system pressure with the outside air pressure. It's best to drain the water separator after the truck has been shut off a while and before starting.

 

DFO,the fact you cannot drain it with a running engine doesn't surprise me.

That's just your fuelpump doing it's work.
So do it without a running engine.

About the fuelcaps and your tanks.
It is a longshot but it is so easy to check.
Just drive till 1/3 or 1/2 tank has gone,open cap and listen.
Repeat for tank N°2.
Total effort .............40 seconds.

If you hear nothing at either cap,then try KC's solution.

 

Thats a alliance water sepperator used on alot of frieghtliner vehicles. As a previous person stated you can loosen the whole filter then drain the bottom. When your done tighten filter again and if you have a primer pump, pump it afew times. This is a primary filter there will be one mounted on the engine as well. As long as you don't loosen the engine mounted secondary fuel filter you should be pretty safe. Todays engines prime up pretty good even if they suck some air after filter changes after a couple cranking cycles they will start.