The normal workflow is to complete the 2D design and then to use some form of CAM program to generate the Gcode.It is the CAM program that will contain the tool library and it's associated speeds and feeds.It will also take the toolpath information through a post processor that will add information about whether the part is intended for metric or imperial units and the distance by which the toolpath has to be offset to compensate for the tool radius.There will be other statements added to move the tool clear of the part when transitioning from one area to another without ploughing through the part and to start and stop the spindle motor.

Mach 3 is a bit outmoded now,but a lot of users are persevering with it largely due,I suspect, to familiarity.Alternatives are UCCNC or LinuxCNC and at a push GRBL or one of the other Arduino based solutions.I have to say that having watched a few Arduino based systems running in youtube videos they might be improved by having a three second delay included in the program after starting the spindle motor as they seem to still be ramping up to speed as the cut starts.
Did the suppliers of the machine neglect to provide training or recommendations about software?