@copperpipe -- Unfortunately, you've hit the nail on the head. That's why cancers in the abdominal cavity can be so hard to treat, since they are often diagnosed so late.
Since the abdominal cavity (and the organs in it) are not visible to the eye, oftentimes a tumor can grow to be quite a large size before it actually starts affecting the body to the point where the person notices it.
The same applies for cysts. In the case of a pancreatic cyst, people can live with them for years before they start causing problems.
To answer your question, one of the ways that they figure out the difference once a lump is found is by a biopsy. In the case of a pancreatic cyst, a fluid analysis will be performed on samples removed from the cyst, which can tell the doctors more about what's going on.
If cancerous cells show up in the biopsy, then of course another course of treatment would be recommended.
Excellent question, though -- I can tell you really know a lot about abdominal issues. And great article too -- this really did provide an excellent overview of pancreatic cysts without being either too technical or too sensationalist.