Hi Chris,
If you have defined your default tool library in the options, then the tools should be there for different sessions. I know they are for me.
As for changing the defaults within the specific cutter path dialogues, I don't believe that is possible at this point in time. However, watch for that in the future. MadCAM 5 is going to offer some new ways of doing things that should prove quite beneficial. I don't want to say too much, and I have yet to see an initial WIP, so I can't say specifically that your request will be there right away. However, discussions with Joakim on the subject of madCAM 5 have me pretty excited about the future of madCAM.
Dan