As with so many of these things there is no right and wrong and I do not use such a device but I do tie a pencil to a block of wood and use it in exactly the same way as you would your device.
I'll describe the process I used with two of my grey hull models with a black boot topping and a red antifouling lower hull. You first of all need to make a stand for the model that holds it firmly then you need to set the stand up so that the waterline is parallel to the work surface it is sat on. You should be able to do this from the plan and set the correct height at the forward and aft ends. If you haven't got as plan then you will have to judge it yourself.
Spray the upper hull colour, in my case good old Halfords grey primer for the upper section, then sit the model in the stand with the model on a large flat surface. Adjust the pencil height in your device to the top line of the boot topping then very lightly slide the base around your model gently marking the hull as you drag it. It doesn't need to be heavy as you move the pencil and it doesn't even need to be a solid line but it does need to be clearly visible. Once you have gone all the way around the hull the line should match up at either end and you can remove the model and lay masking tape above the line. Use thin tape to ensure that you can follow the line accurately then over lay with a wider tape and finally tape and newspaper to completely mask the top of the model. Then spray your matt black up to the masked line. When dry remove the tape and sit the model in the stand again. Then set your pencil to the lower edge of the boot topping and draw another line around the hull, this time you are drawing on the black paint. Again take the model out of the stand and mask above the new pencil line covering the top of the model completely with newspaper. Then spray your antifouling, in my case again Halfords red primer all over the lower hull.
When you remove the masking tape this time you get a perfect black boot topping seperating the red antifouling and the grey upper hull.
The tricky bit is around the stern but as long as you keep the pressure on the pencil gentle so as not to move it vertically you should get a perfect line. The great beauty of this technique is that it gives you a perfect shape boot topping line which, exactly as on real vessels, actually varies in width according to the shape of the hull. Around the stern particularly if you look at the boot topping square on you wil notice that it is quite a bit wider but if you look at it horizontally it looks to be of equal width. This is infinately better than using tape, which remains of an equal width and never looks correct when viewed horizontally.