Will the 68060 automatically be available when its plugged in?

The 68060 should be available as was with an original Amiga. Make sure you install the proper set of files on your sdcard for the replay from the Github. https://github.com/FPGAArcade/replay_release/tree/master/amiga/amiga_68060
Note: An FPU & MMU will be dependent on what CPU is installed. Eg: a real 68060RC50 will have a real FPU & MMU inside and will be available for the replay to use. If its one of the non FPU/MMU models, then these functions will not be found. Also see the general notes on installing the 060 Daughterboard which amongs’t other things, will show you how to install the 060 libraries. https://www.fpgaarcade.com/kb/how-to-install-and-setup-the-060-daughterboard/