qmc2 saves .ini files in the MESS root folder instead of the ini folder, is there anything I can do about that?
Hmmm, QMC2 does not manage ini files itself (except for the ini-exporter/importer). You may need to set the "inipath" in the global emulator settings, though!
Nothing seems to happen when importing MESS64.ini and I can't find anywhere else to set the ini folder path.
I'm running the qmc2 executable from inside the MESS folder.
OK, so you're really talking about the ini-exporter... yes, it uses the inipath setting or "." if it's unset.
Also, you may want to read this FAQ
for more information about how QMC2 handles the emulator configuration.