2 related questions: making part copies and 2 offset z axes

Sorry for this novice question but am just getting started in making a CNC machine. I haven't used the SW before, I have just read documentation.

1) If I want to make 2 copies of a part, I understand that I can make one copy, change to an offset coordinate systems for the next fixture with G54, regenerate the toolpath and then run again for the next part. The question is do I have to manually intervene and change the coordinate systems between parts being cut or can I use scripts to just cut multiple copies from the start. A liitle confused on how this works.

2) A related question: If I build a machine with 2 routers which are 5 inches apart in the Y direction holding different toolbits (for example a V-cutter and a straight bit) independently controlled Z axes as a 4th axis, how do I tell Mach 3 about the 5 inch offset when using the second router. Do I need to use the G54 offset again or do I just tell Mach 3 about the 5 inch offset once, and then just knows how to deal with it? I plan on getting V-carve pro. I assume Mach is the only SW that needs to know about the 5 inch offset and V-carve pro doesn't care?

Thanks for your help.