I think I understand your question, so I will ramble on a bit. Pick out the bits you need.
In simple milling, you are normally cutting a shape out of a flat material. This involves using and end mill, or a slot drill or some similar tools.
Since they all go in the same chuck, then the path they cut depends on their diameter.
G Code allows you to program the cutter as though it had no diameter, and so what you see on the Mach3 tool screen is the actual program you write.
Tools you use in the mill are entered into the tool table - see Config/Tool Table - and in there, for each tool, you can enter their diameters, lengths etc etc. Wear, which you keep mentioning is also included, but I do not use it, because I measure my tools with calipers, and enter that diameter in the table. I assume the big boys buying super duper tools will have a specified diameter - and add wear in microns or thous as it happens to maintain absolute accuracy.
Tools are changed by codes M6 T** the numbers following the T is the tool number in the table. The M6 code can be programmed to do several things - nothing, move to a specific location for a manual change, or operate an automatic tool changer.
Cutting a simple outline - and allowing for the tool diameter is G41 or G42 - G41 is with the tool on the left, G42 is with the tool on the right - G40 cancels the compensation.
All you do is, at the begining of the program enter G41 - and from there until a G40 cancellation, the machine will alow for the tool width of the tool that is currently being used. It changes the compensation if a new tool is added.
I do not understand, when you say you want to use "wear" to change the part dimensionally when you cut it - how many go's are you having. In theory if your machine is set up accurately, and you draw you part accurately, then the machine will cut it accurately, without, as we used to do manually - working up to the finished diameter in little cuts.
Machines can be programmed to take roughing cuts and then change tools and take a fine finish at exactly the right diameter or whatever.
Have a look through the codes on Mach3 Mill and you will see what I mean. Have a look through Mach3 Config as well.