Kent - glad you have it sorted. The tool length is not important - if you are using one tool - or if you touch the work with the tool tip and zero everything. The machine needs to know where it is in all respects.
It is the same with limits and homing. You can set soft limits which will stop your machine banging the physical extremeties of the machine, and, as you say, knocking everything out of kilter.
As for homing - I do not bother, since I much prefer to set each piece of work manually before I cut it. If you are in a high cost, low volume scenario, I think this is better - i.e I like to know I've checked evrything before setting the machine off - it saves ruining a piece of work that I might have spent some time on beforehand.
If it is low cost, high volume, then yes - get the machine to go to a home, throw in a workpice and press the button. If you spoil the odd piece it doesn't matter.
You will probably come up against another offset shortly - I assume you have set up backlash - that is tool width. If you are doing circles and other complex scrolls, you will have to take notice of tool width and set the machine to compensate for it. - it is great fun to watch the machine cutting something you have designed.
Jim.