Disclaimer up front: It's been a while, and I don't remember exactly how or where I originally learned the "proper" technique, and I also can't really speak to the "why" without speculating.
In a former life, I was a mobile electronics installation technician and spent about 7+ years professionally installing car audio systems, remote starters, alarms, overhead video systems, etc. I've crimped a pretty wide variety of connections for vehicle wiring, from 0 awg power cables to 22 awg wires. I haven't had a chance to do much wiring on our plane yet, but am excited for that phase because it is one of the few areas of the build I will have some prior experience in
I believe the expression we used is "saddle the seam" or "seam-to-saddle", in other words the curved part of the crimper goes over the seam, and the tooth on the crimper should penetrate the back (non-seamed) side of the terminal.
There is also some debate, not unlike with primers, over what kind of crimper to use, and when to use it. For instance, some say not to use a "toothed" crimper on insulated terminals, or not to use them on sizes larger than x-awg. Personally I've always had good luck with toothed crimpers, particularly on smaller connections, but there are some gotchas you have to be careful of especially with insulated terminals.
An even better way to crimp large-diameter wire, though, is going to be with a hydraulic crimp tool that uses a hexagonal die. The tool you are using is definitely adequate, but the way the terminals "squash" they will only hold the top and bottom very well, and be relatively loose by comparison on the sides. Also, it's harder to make every crimp perfect every time. After making all the heavy-gauge crimps necessary to do your whole plane, you're going to be pretty worn out from doing them all manually, and they may not all be 100% consistent.
In my opinion even a cheap hydraulic crimper with the proper die will do you good. I'd recommend this one, or something similar to make higher-quality and consistent crimps on your power cables:
http://www.amazon.com/TEMCo-Hydraulic-Cable-Crimper-TH0005/dp/B00HJXG3KM
Cheers and happy crimping!