The easy way is with a mortise bit with shaft mounted bearing of the same o d as the bit. Then all you have to do is take a straight edge and line it up with your dado marks. You can still do it with one without a bearing (using a straight edge) but you have to measure the offset between the bit and the edge of the router’s base and move the straight edge over that much.
As was mentioned, plywood is never exactly the thickness it is sold for. It starts out that way but then gets sanded smooth which leaves it undersize. Your best bet is to use a bit smaller than the ply, for example a 1/2” bit for 3/4 ply, and rout both sides of the channel separately.
Someone I consider a master woodworker once told me that a master woodworker is not someone who never makes mistakes. He is someone who is able to cover them up so that no one can tell.