If you prefer winuae, then install the system under winuae, and when you finished, take the hardfile, or the directory (if you don't make hardfile)and put it in your MOS system.
Editing the config file for uae is simple. There are some samples in conf directory. The trick is te following, if you using directory, thet fisrt you set the device (for example dh0:, and after you set the long path which is in your system. so not just the directory in your progdir. for example: dh2:emulators/euae/harddisks/system/
MorphOS PowerBook G4 1,67GHz, 2GB Ram, 250GBHdd, ATI 9700/128MB
Morphos G5 2,7GHz, 8GB Ram, 500GB Hdd, ATi Passive cooled 9800 PRO/128MB