Vacuum leaks are the most common failure that causes negative pressure system errors. If you don't have any starting point (recent changes, parts replaced, etc) you will have to start at the pump and replace connections or tubing one at a time until you hit the subtanks.
If you do have an idea of what changed recently, look around that. A negative pressure gauge is also helpful for diagnosing leaks, since you can hook it up to the line and see if you have a leak before that point or not.