Unfortunately, there's all kinds of things that you need to deal with:
1 Intention of the scope.
2 Acceptable obstruction ratio of the system.
3 Acceptable amount of light loss in the off-axis images.
The illumination circles are intended to indicate how much light from the primary actually gets to that spot on the focal plane. As a result, there is a diameter of 100% of the light from the primary going to the focal plane. This limit is set by how big the secondary is relative to the other dimensions. Then, as another indicator of what may be acceptable, the 75% circle is also given as this is the diameter of a circle which has that much light from the primary striking the focal plane. The optimum for getting light to the EP would be a 100% circle large enough to fill the largest FOV EP (which would be about 1 1/8" or a bit less for a 1 1/4" EP) but this runs into problems of a larger secondary which means more obstruction to the light coming into the scope and lower contrast (actually a quite small number which nobody quantizes as they usually don't know what it is) due to the larger obstruction causing an enlarged Airy disk.
In truth, you can vary the secondary size by a fair bit before you start running into troubles either way. I would recommend that you make the 75% circle about the size of the focuser for the average scope design, the 100% circle about 1/4" or so for a planetary scope and if you just want light for a camera, make the 100% zone the size of the focuser tube.
Newt makes a very nice set of visual drawings in addition to the numbers so you can really look at what is going on. As a side benifit, it gives the baffle sizes that are needed to properly baffle the telescope. If you really want to play around, make it do an F3 design and look at the offset of the secondary and so forth.