The Drain water seperator is very important!!!! Ypu need to drain the water out of the rail fuel filter which is under the cab on the driver side. If oyu have an owners manual it will tell you how to do it. It is easy to do but you do not want to keep driving it with that message on or you will do serious damage to the engine. You should drain that filter once a month!!
Cleaning the exhaust filter is the regen process. You can search both the water seperator and the dpf and you will get plenty of information on both. The owners manual has all this in it you should read it. If you do not have one you can go to Official Ford, Lincoln & Mercury Owner Site | Personalized Owner Information | FLMowner.com
and register your truck and all the information will be on there as well. Good Luck to you and welcome to the forum.