New milling motor Proxxon FBS 240/E upgrade to Kress 1050 FME-1

[JAZZCNC]

So i have a g-code file from SheetCam and it was programmed for say a 6mm roughing cut leaving an allowance for finish, do i need to make a second file for the finish cut or do you use the same cutter but just program a final cut for the finish pass??

Just one file for both operations.
If corner radius are larger than the roughing cutter and the flutes edges are good enough for finish then use same tool. If not then just use smaller tool for the finish so it can clear the corners, always use a tool just little smaller than the corner radius. But in both cases it can all be done in one file.

One job i have in mind has some 3mm holes in it, i would be looking at ramping in with a 2 or 2.5mm tool for them and then do the outside profile with a larger tool maybe - I am lacking knowledge of how you change tool and get back to exactly the right place OR do you use the tool dia offsets in Mach3

With circler pockets or holes Spiral rather than ramp if possible.
When you change tools the G-code file just stops tells you to change the tool and waits for you. You then can jog the machine to easy position to change the tool. After changing the tool you reset the new Z height by touching off the material again and setting zero. Then just press cycle start and the cutting continues.
The Cam software will have taken care of tool offsets when created the g-code.