Rich - You are getting worked up over nothing. The buttons you are talking about have nothing to do with getting started.
I must assume you have some knowledge of machining, such as cutting speeds, traverse speeds etc etc and are used to these. You can go through Mach3 configuration and set as many of these as you can. If you do not understand it, leave it alone. The majority of entries do not interfere with the normal operation of the machine.
To answer a couple of your queries - the machine needs to know where it is all the time. It keeps track of it's movements. It stores these positions in the Machine C0-0rdinates DRO's. However, machine co-ordinates are not particularly useful to us, the operators. We are probably more concerned with the position of the machine in relation to our work, and the program.
The Machine Coords buttons swaps between the two types of read-out. When lit it is showing the "raw" machine position. When not lit it is showing a more sophistacated position (which depends on several factors).
The "Ref all home" button is part of the positioning. If you have "home" switches fitted to your machine (They are NOT necessary) you can hit this button, and the machine will go to each switch in turn, stop at the position and zero the DROs.
This sounds great, but, whilst it might be alright for the big boys, in practice it is somewhat limiting - since it means all your work, all your programs etc have to start from that position. If your machine moves at the speed of light, then this is no problem. My home switches ( which I hardly ever use now) are fitted underneath the chuck, with the lathe table as far towards me as possible. It was really the only place to fit them. At the speed of travel of my table, it takes two minutes for the thing to get back to a position where it can do any useful work.
If you do not have home switches activated in the ports and pins table, the hitting this switch zeros the DROs, so the best plan of action is to move the table to a convenient position for your work (say bottom left hand corner) then hit the ref all home and the DROs go to zero - a nice place to start.
Worrying about the positional side of things is not the place to start - it is too complicated.
Concentrate on placing a workpiece on your table. Jogging the axis to touch the start point - bear in mind the thickness of the tool. Setting the DROs (just type in the numbers and hit return) to the correct start position (normally Z, the cutting tool rests on the workpiece (this is z=0), and then moving the table about. The DROs will always show your relative position from the start position.
You can then move your tool manually using G0 and G1 commands. You can expand this and perhaps write a G Code program to move the tool from 0.0.0 to the centre of one side of the work piece, then bring down the tool 10 thou, start the tool, and cut a grove along, up down ( in fact anywhere you want) and finally return to position 0,0,0.
Once you can do this, you understand what CNC is all about - there are other moves, arcs of circles to the left or right, and some specialist drilling moves, but basically G0, G1, G2 and G3 cover the vast majority of moves. All the rest is just icing on the cake, and things you will pick up as you go along - because you have got to that position where you need to know to enhance your program.
These things sound very basic, but unless you understand the fundamentals, using these super dooper programs to produce reams of G Code will be a mystery.