It is typical to focus to the top surface, unless cutting thick material in which case you may want to focus a bit deeper. The Epilog has a removal gauge and you should “just be able” to slide a sheet of paper between the gauge and working surface for proper focus…, assuming the tech everything set correctly.
The Epilogs have both the honeycomb and perforated metal, but I always use the honeycomb.
From Epilog:
"The Vector Cutting Table is used to lift the material being cut above the work surface. This allows the laser beam to pass cleanly through the material you are cutting and dramatically reduces underside reflections. The air space below the vector grid is connected to the exhaust, so smoke is removed not only from the top side of the material, but also from the underside.
Our Integrated Vector Cutting Table is included standard in the Legend Series and is a robust 1" (25.4 mm) thick. Simply remove the Task Plate and place the Vector Cutting Table in the system to dramatically reduce underside reflections from burning the back side of the material being cut."
BTW, the biggest bug-a-boo with these tables is that they tend to sag in the center. This then makes the beam go out of focus and it may not cut all the way through the piece.
If it doesn’t, and the piece has moved at all either because of the sag, or because of human intervention, it has just become scrap because you really can’t complete a cut that has not gone all the way through.
Also, depending on in order in which things cut (and you have almost no say in this matter), cut lines can make a piece sag before the remainder of that piece is cut out leading to pieces that are under or oversized, or lines that don’t line up.
I made a shim out of brass to compensate, but that only does so much.