Kyle,
Welcome to the Grumble!
It's too bad that you didn't ask some of these questions
before you bought your chop saw, you may have saved yourself some money and alot of headaches by asking first and buying based on the answers received.
(That's as delicately as I can get this early in the morning!)
I doubt that you will find a half dozen framers who would recommend buying a saw that large for the average sized frameshop. There are alot of problems with buying a saw that large including price, availability of blades, runout while operating the saw, and a few more which probably will come to mind later.
The most common sizes for chop saws are 10" and 12" and either will handle up to 85% of the mouldings sold in most of your average sized shops. If you sell alot of large moulding, say up to 4 1/2" or so, I would recommend the 12" saw but, in my dealings with photographers over the years, I haven't had the pleasure of selling that many large expensive frames to them. It is usually the other direction that they head.
I have had a Phaedra setup since I started framing in the late 80's and am totally pleased with its operation and maintenance. But I wouldn't recommend it for any type of high volume output of frames. I have 2 saws set up on it in tandem but there are still too many extra cuts to be made per frame to warrant using it over a dedicated saw system built to make 2 cuts per pass on the moulding.
Setting up the Phaedra was simple if I remember correctly. It's been many years ago since I set the decals on my calibration table (when I bought mine they only had one set of decals on the left hand table). I think I simply mitered something like a 12" length of moulding to exact measurement, lowered the saw blade down, butted the moulding against the blade, and slid the decal under the moulding until the 12" calibration mark lined up exactly with the edge of the moulding. Then I carefully removed the backing and applied the decal down to that same spot. Once you have it set up for any given length of moulding, it should be right for all other lengths and widths of moulding.
I am sure that there are a few easier methods of aligning the decals today but that seems to be the way we did it back then.
Good luck.
Framerguy