I use macros to manage my cross-class skills.

For example, my base cross class skills:
/aaction "Byregot's Blessing" on
/aaction "Steady Hand II" on
/aaction "Comfort Zone" on
/aaction "Hasty Touch" on
/aaction "Careful Synthesis II" on
Then when I want to do lv60-2* crafts I use this:
/aaction "Manipulation" on
/aaction "Innovation" on
/aaction "Ingenuity II" on
/aaction "Muscle Memory" on
/aaction "Tricks of the Trade" on
/aaction "Waste Not II" on
/aaction "Reclaim" on
and if I want to do 3* crafts I use this:
/aaction "Maker's Mark" on
/aaction "Flawless Synthesis" on
/aaction "Waste Not II" on
/aaction "Piece by Piece" on
/aaction "Tricks of the Trade" on
/aaction "Reclaim" on
/aaction "Innovation" on
/aaction "Ingenuity II" on
and if I want to swap between the two I use this
/aaction "Muscle Memory" off
/aaction "Waste Not II" off
/aaction "Ingenuity II" off
/aaction "Piece by Piece" off
/aaction "Innovation" off
/aaction "Manipulation" off
/aaction "Tricks of the Trade" off
/aaction "Reclaim" off
/aaction "Maker's Mark" off
/aaction "Flawless Synthesis" off
Makes swapping just a matter of waiting 15 seconds or so.