I have the same bits.
You drill with the small part and just barely kiss the topsheet with the large part to guard against mushrooming.
I did put tape on the tap for depth.
Plugs for previous holes, plastic usually but wood if drilling nearby.
The blue fixture is for vertical holes -- so far I've always had a drill press available and haven't used the fixture.
I use a micrometer caliper as a square to bring the locations of the edges up to the top, so I can find the true edge-to-edge center.
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