This question came up elsewhere, and i found it quite useful - so here it is
Sometimes you may want to boot directly into a different core - eg Minimig - which can be achived with the following "trick":
first, create a little BASIC program, which contains the following:
you can create this on your PC by pasting the above into a textfile, then convert it into an actual BASIC program using "petcat", which comes with the VICE emulator (there are other tools for this as well, but this is what i use and know works):
now copy the resulting boot.prg to (for example) the SD card that contains your minimig setup.
enable "boot from SD card" in the chameleon settings, save settings
insert that SD card, and powercycle the chameleon.
voila - straight boot into the core you selected in the BASIC program. This way you can make yourself seperate SD cards for each system, and boot into the right core automatically.