You don't have to see the clip. Just push the tool in behind, from the same angle as the handle points. That's the way they're always lined up. Why do you think the handle of the tool is so long? To reach past the crank handle.
The tool will grab the outter ends of the "C", and spread it and push it off. When you're done, put the clip back on the crank, then just rotate it until the splines mesh, and push it back on.
Here's a couple pics that should help;
They're always mounted in this direction;
http://i.ehow.com/images/a02/0f/bv/install-car-window-crank-handles-1.3-800X800.jpg
This is on a different kind of handle (door opening handle), but it shows good how it works;
http://image.superchevy.com/f/17294487/sucp_0803_09_z+aftermarket_specialty_tools+window_crank_handle.jpg
You shouldn't push the panel back at all, or pull on the handle. Just slip the tool in between, from the direction of the knob, and it virtually does the rest of the job itself.