1) I strongly consider mutation allocation pre-game. I can set up 4 models (including 1 Jackalope) with mutations t1, that puts a cap on how many beasts I can reasonably hire. And when hiring them I try to have a spread of them to have enough "optimal" mutations for everyone. [edit: I can do more, but 2ap for 4 mutations is my comfort zone in this regard]
2) I don't necessarily have all my mutations attached ever, but most for sure. Standard operating procedure is: 4 mutations via Chimeramancy, 1 via Marcus, 1-2 via Myranda (and Order Initiate). T2 I add another 2 mutations. Assuming single Myranda/Initiate, that's 8 mutations down. T3 I might add another mutation or two but often I can't spare the AP. Depends on the game state. T3 mutations go on Jackalope and if I absolutely need something on someone else.
Cerberus gets Camouflage/Wings/Serrated, usually one of the first two. Really depends on what my opponent has.
Blessed of December gets Camouflage, Wings or Horns.
Slate Ridge Mauler gets Armour t1 and Horns t2.
4) Jackalope gets Serrated and then any left overs. Often Horns or armour. Actual mutation effects are secondary.
5) Marcus tends to obey charges and try to set up adversary (not necessarily with his own attacks), then companion into a beater beast. Often he plays in bit of an offensive bubble with Jackalope and Bear or some other beast. But he's flexible, double walking 14" and Interacting is certainly a thing I've done. I don't use a whole lot of chimeramancy in t3+, apart from on Jackalope. Admittedly I've been a bit lazy with Adaptive Evolution, so that might well change in the future.