To use MakeFat, you must have a 68k and PPP appication with identical resources (except for the CODE, DATA and cfrg resources) named something like WonderApp68k and WonderAppPPC. Drop these two applications on to MakeFat, and it will generate the FAT version and call it WonderApp (cheerfully overwriting any existing file called WonderApp, so be careful).
So to use Metrowerks CodeWarrior to generate a fat application, you have two projects, one 68k which generates WonderApp68k and one PPC which generates WonderAppPPC. The two projects should have exactly the same resources. Either one should be able to run by itself (although the PPC one obviously wont run on a 68k mac, and the 68k one might not be able to run on a PPC mac if you do something weird). Then use MakeFat to combine the two in to a single application.
All MakeFat does is a lot of error checking, followed by duplicating WonderApp68k to WonderApp, and then copying the data fork and cfrg resources from WonderAppPPC to WonderApp. Very simple really. Source code is available from <ftp://mirrors.aol.com/pub/peterlewis/source/>.
The program has no user interface, just drag two apps on to it, it processes them and quits. If you launch it without any apps, it will compain.