Ah, sounds like the machine is a bit different from ours, apparently the fiducial camera system is optional. Our machine has no metal pins and I have to drill 4 fiducial holes as the very first stage of any board I mill. Using metal pins to lock the board in place sounds a lot easier. Does it have the vacuum cleaner option?
Depending on the software setting, you will see this box everytime a tool is changed.
I am using the camera to measure the width of the trench "universal cutter 0.2 mm (8 mil)" (orange plastic ring). I do have a monocular microscope too but I find it too inconvenient to use since it needs a strong light source. Anyway, to adjust the depth of the cutting tool you will typically mill a short line somewhere where it doesn't interfere with your board (right next to it is fine) and measure the depth. (move the head into pause/parking position etc to open the cabinet)
A screenshot of the camera measuring the width of the universal cutter. I can mark two spots with the mouse and the software will display a delta x / delta y.
There's a metal ring/adjustment wheel around the dremel tool which you can turn clockwise to lower the tool and counterclockwise to lift it. The wheel is rather stiff but has identifiable increments. Turn it a few clicks, like five or so, to tune the depth and repeat milling a line/measuring until satisfied. You can actually see this in the first picture of my previous post. I milled like 4 mm or something, adjusted the depth and milled another 4 mm to the right and was satisfied with the width.
In short: Select a spot where you will mill a short line manually.
Start the motor (vacuum starts), lower the head, use the arrow keys in the software to move the head a short distance, lift the head, stop the motor and move the head into pause/parking position, open the cabinet and check the width. Repeat until satisfied.
The main tool (universal cutter) typically lasts 30000...40000 mm. We set the threshold to 30000 but as they are a bit expensive, you can try to squeeze out a little more. Worst thing to happen is that the tool breaks and simply won't cut at all. Be sure to monitor the quality of the cut.
Here's the tool setup we use at the moment, note the "Maximum [mm]" number of each tool. For drills this means number of holes drilled.
I marked the buttons needed to adjust the tool (attached higher quality version as a file)