I had to modify my JMI case to accomododate my 12" telescope with the Get-A-Grip handles. The process isn't complete - I still need to fashion some covers for the protruding handles, but the small holes in the case are not a big deal. The holes are a bit larger than they could be since I am planning on eventually covering them, so I was not too worried about getting a snug fit with the padding.
The handles are on the far side of the telescope yoke. This, when the telescope is placed 'face down' in the case, means that the Get-A-Grip handles are facing up. The top was the half of the case that needed modification.
I started the process by installing the handles, placing the telescope into the case and pressing the cover down some on the handles to make impressions on the foam. That gave me an idea on where to start cutting the foam out. I used a snap-blade knife (a razor knife with an extendable blade to snap off portions to remain sharp) to cut the foam out. Any sharp knife would work.
Once I got down to the shell, I then drilled a series of holes using a 1/4" drill bit from the inside of the case to define the premiter of the hole. Then, from the outside of the case, I used the snap-blade knife to cut out the waste material of the shell, leaving what you see in the photos. I was also able to fine-tune the holes on the angled side of the handles. You don't want the case shell in contact with the handles. It would chafe them and transmit impact vibrations to the scope more directly.
I guess I could have used a jigsaw, but I did not want to tear up the case. A metal cutting blade in the saw would minimize tearing. The plastic of the shell is soft enough to carve, with the knife, and you would probably want to do that with the sides left by the jigsaw to smooth them out.