I believe Shoo Goo and Aquaseal are very similar products, maybe different formulations of the same compounds. Shoo Goo, if I remember right, is a little thicker and harder to work with in tight spaces (like sealing the inside "seams" on a 3-corner tear), but is excellent for exterior patches on high wear areas (like worn out feet or knees on neoprene waders).
For larger tears, I'd suggest holding the tear together with duct tape or something similar, then patching the other side. After the Aquaseal sets, pull off the tape and patch the taped side, too. For larger tears, you may want to back up the aquaseal with a cloth patch. If abrasion is a concern, a post-repair coating of shoo goo provides a nice barrier layer.
Aquaseal is great for patching tears, and Shoo Goo or Aquaseal for dealing with worn spots, but if you have leaky seams, you can drive yourself nuts and cause brain damage from breathing toluene fumes, but you probably won't get a water tight repair unless you can isolate the source(s) of the leak--and then only if the leaky part of the seam is pretty small. In my experience, when the seams go on waders, they go all at once, and repair is pretty hopeless.