Mountainman,
If your machine has only a little backlash and can handle climb milling, then I would climb mill the part the whole time. Conventional milling has the cutting edge sliding over the surface until the material is thick enough to peel a chip. This wears the cutter much faster. Climb milling starts with a full chip and the chip thins until it breaks off, which is much better. In most cases the finish is better too.
When programming manually from a CAD drawing I always program right on size and use cutter comp. I always put the tool path in a subroutine and just set cutter comp, call the sub, adjust comp, call the sub. I program the subs in incremental. That way I can always position it anywhere, or even use it in multiple locations. I also like to use undersize cutters on pockets to sweep the corners with the cut, not crash to a stop and change direction. This got me on good terms with the guy in the tool room because I actually asked for resharpened end mills, and he always made sure I got freshly sharpened ones. He did a good job too, they always seemed to cut better than new ones.
One of the machinists said I was wasting time with rapid moves back to the start of the tool path and should program it the way you want to. I pointed out to him that if we had lots of parts to do that would be a good idea. With batches of ten or less you really can't justify the extra coding and testing to be sure it works.
Gary H. Lucas