CNC Process

I am new to using a CNC machine. I built a small (made of wood) 3
axis mill so I could play and learn with. Later I will purchase a
Drill/Mill and convert it. As of today I am using CNC-Pro

I don't have any problems with the CAD/CAM software side of things.
It is running the machine that has me stumped. The areas that I have
questions are:

1. Home position.... When I press the Home button it moves my
axis all the way to one side and sets the coordanants to 0,0,0 should
this be left at 0,0,0 or should I touch my tool on top of the material
and call that 0 in the z-axis?

2. When I need to change a tool I will loose the z-axis tool
location. do I again touch the tool on the top of the part for z=0 or
should I re-home?

3. If I rough the part and loose the top of the material (by cutting
away all the material on top) How can I set the tool again?

I am so confused about setting the machine up for a job. I have the
limit (home switches) set at the far positive position in all axis. Z
moves up. X table moves to the left. Y table moves to me. So this
means that the tool in relation to the table will move Z-up, X-right,
Y-Away.

When I use the homing feature it sets 0,0,0 at the home position.
This means that I always cut in the negative space. Is this correct?
What is the best method?

Thanks

CADMAN