Put the upper panel of MDF on your glue-up surface, bottom side up. Put the bottom panel of MDF on your other surface, bottom side down. (The panel with the holes drilled in it is the bottom panel, and the side that has the your layout diagram on it is the bottom side.) Chuck up in your drill the appropriate driver bit for the screws your using. Make sure you have a freshly-charged battery, and crank the speed down and the torque way down. You don't want to over-tighten the screws, MDF strips easily.
Of course, I, on the other hand, with my Ikea oak countertop, probable went overboard in the other direction. Since I needed to trim the countertop to width,I figured I'd take off a couple of 1/2" strips to use for edging the MDF. I clamped the countertop to my bench base, and used the long cutting guide. I'd asked around for advice on cutting this large a piece of oak, and was told to try a Freud Diablo 40-tooth blade in my circular saw. I found one at my local home center, at a reasonable price, and it worked very well.
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