"nuxeo.conf" file in the same location as the nuxeoctl.bat file.
To launch multiple instances of Nuxeo you need to:
Remove the registry key (set up by the Windows installer)
Have wrappers around NuxeoCtl.exe/nuxeoctl.bat that define different NUXEO_CONF environment variables.
Note: You'd also want to have different nuxeo.data.dir, nuxeo.log.dir, nuxeo.tmp.dir, nuxeo.server.http.port and nuxeo.server.tomcat-admin.port in the two nuxeo.conf files (you can set nuxeo.server.ajp.port to 0 to disable AJP if you don't use it).