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If I understand you, you want to make a double rabbet joint?
A better, simpler, and stronger joint would be to route the ends of two sides 3/4 x 1/2 leaving a lip of 1/4 inch thick protruding 3/4 inch. If I understand the bit you have this should be easy enough.
Leave the ends of the other two sides alone. These ends will sit-in the rabbets you cut.
Join using the recommended epoxy, plywood has 1/2 end grain typically and end grain makes a very poor joint. Don’t use too much epoxy, and clamp it.
After its dry, drill and countersink screws to reinforce, being careful. If you’re using 3/4 inch for the bottom do the same thing.
Not real sure where a jig saw comes into all of this.
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