If you are building several different sets of output files using several different types of sources, then you could create several different build targets, each using different access paths, to load in the proper files. From the looks of it, though, all outputs land into the /bin directory, or the directory specified in the Target Settings panel's Output Directory setting. You'd select one build target, do the build, remove the output file to a safe directory, select the second build taget, do the build, move the output file again, and so on. It doesn't appear that you can specify mulitiple directories for the output, however.
Another possibility is that CodeWarrior does provide command line tool support, so you could write a script that could specify a different output directory for each build, assuming you're building different programs as describe above. If you're trying to make one program all at once, I don' think that's possible.
---Tom