If you watch the Video Tutorials there is a program on "Scripting" which covers this exact problem.
The M6 script can be altered to do precisely what you want - in other words - move to a preset location and wait til you have reset the tool. You can jog the tool up and down onto a plate or measure or what ever, change the z axis offset and resume.
The script is in Visual Basic and is fairly easy to learn - if you know any of the programming languages, and the scripts themselves can write GCode to move the mill directly.
I have this on my lathe (slightly different command but) - the tool away from the work, I change the tool and the tool number changes which brings into effect the new tool offsets. I have a quick change holder, so my tools and offsets are all preset - but that is something for you to think of in the future.