It's less messy to just use your hands. With careful technique, of course. Especially if you start out using your hands, instead of trying a spoon first - somehow it always ends up way messier if your start with a spoon and switch to hands, than if you start out intending to use your hands.
The easy way to stuff manicotti to grab a little chunk of filling - somewhere between a rounded tsp and tbs, the maximum is the diameter of your manicotti - maybe roughly tap it into a ball, hold the manicotti in your other hand (maybe rest against the filling-bowl), and tuck the filling down one side of the manicotti. If the filling is a bit more sticky, you will have it scooped on your fingertips, and can use your thumb to push the filling down from your finger-fronts. Repeat until your manicotti is filled,maybe tucking the last few bits on the other side of your manicotti if the filling didn't stuff down quite evenly.
You should not be making a mess of your counter-tops, or getting filling anywhere other than the bowl and manicotti. Once you've got a bit of practice, you might not even be making a big mess of your hands - you're just using your fingertips, on little blobs of filling at a time, you palm should stay clean and dry for quite some time.
The stuffing goes very quickly, since even though you're grabbing only a bit of filling at a time, it's really quick to scoop a tiny bit out. It's easier to control the filling when you're only dealing with a bit at at time, it doesn't drop bits off or smear around like when you're trying to fit a handful in at once. And using your hands is much more intuitive than a spoon or even gloved hands - yeah, it feels messy when you first dip your fingers in, but actually the mess always ends up less because the filling is easier to control with your fingertips. And, I'm not sure why - but starting with a spoon and moving to fingers is always messier than starting with fingers. Not even just when using the spoon, too - maybe something about being impatient or a less careful mindset that starts with the choice of spoon and spills over?