"OK....so how would I home the tool to a work piece?"
Again, I will tell how I do it as there are several methods running around. First, I home the machine (machine coordinates G53) and then using a probe, I find the home position of the work piece X0 Y0 Z0 and this is generally in workspace offset G54. All machining is done in G54 offsets but the machine will automatically think in machine coordinates especially as far as limits etc.



"Also, can someone please clarify the directions of drives in relation to axis movement? I had assumed that on the X-axis, the table would travel from right to left when in +dir, the Y-axis would travel from the front (nearest handle) to the back (nearest column) when in +dir and the Z-axis would be travelling vertically down in +dir. Is that correct, incorrect, or does it simply depend on whatever we want our machines to do? Are there conventions, or do we just build whatever seem right?"

First off, "convention" is to think the spindle is moving and not the table! I know sounds confusing to begin with, but shortly becomes second nature. Convention can be what you want, but "most" think of the spindle being over the lower left corner of the table as X0Y0. BUT the main thing is to set a standard for yourself and stick to it. I personally like this convention as I am most always now working in positive values for X and Y. As for Z, convention is the top of the travel is Z0 and your always working in negative directions.
This is especially true of the cam programs that I am familiar with.