I was worried about making the square cutouts for my panel too but it turned out to be not as terrible as I thought. I used a jigsaw as well with a fine toothed blade and it cut through the thick steel quite easily.
I first measured and drew out the squares, then used a 1/8" drill bit to drill pilot holes at least 1/4" from two of the corners. Then I widened the hole with a step bit until it was large enough to take the jigsaw blade. Cut along toward the corner without the hole, gently curving to intersect the cut line. Don't try to curve too much or the blade will bind up. Once you reach the far corner, turn the panel around and cut back across the same line, this time not curving back to your hole.
I intentionally cut a hair smaller than I needed because I was worried about taking out too much material and messing the whole thing up. I'll caution you to not be too conservative as removing the material takes a lot of time. To get to just the right size, I used a grinding wheel on the dremel to expand the square out to the proper dimensions. I found it easier to not clean up the corners using the grinding wheel, instead switching back to the jigsaw to nibble out the last bit.
Each hole took about 10 minutes. The first one took about an hour because I made the hole far too small and it took forever to grind it to size.