I had a couple of stuffed shells with my dinner tonight, and they were pretty tasty. However, I ran into the same problem I always have when eating them. By the time I’m done with one my plate is a big mess of sauce and cheese. Those things just do not stay together! To give you a mental image of what is going on here, imagine if water balloons were edible and you were trying to eat one with a fork.
Is there some secret trick I’m missing here?
I don’t know what size shell you’re stuffing,but it sounds like the macaroni may be overcooked.
The smaller size lets you eat it with one bite,if you must cook it beyond * al dente *,so you don’t lose any of the cheese.
And if you do wind up with some sauce and cheese left on your plate,that’s what Italian bread was made for.
If you’re too polite to mop it up with the bread just feign an oops,I dropped the bread onto my plate 
It may have been overcooked, and the shells are pretty large, but I can’t do much about that since all my food is cooked by the university dining hall staff.
I usually eat the filling (cheese and/or meat) out of the shells with my fork, then cut the pasta shells with the side of my fork and eat them that way. I find it to be the neatest.
But I’m the kind of person who literally cleans every plate of food in front of me. I’ll slide pasta or bread around until every drop of sauce or grain of rice is gone. Your mileage may vary.