The create-plugin script doesn't create a Config.groovy but if you create one yourself it will be used. Don't copy one from an existing app since it'll be cluttered with stuff that isn't applicable, just create a log4j closure and whatever other properties you need:
log4j = {
error 'org.codehaus.groovy.grails.web.servlet', // controllers
'org.codehaus.groovy.grails.web.pages', // GSP
'org.codehaus.groovy.grails.web.sitemesh', // layouts
'org.codehaus.groovy.grails.web.mapping.filter', // URL mapping
'org.codehaus.groovy.grails.web.mapping', // URL mapping
'org.codehaus.groovy.grails.commons', // core / classloading
'org.codehaus.groovy.grails.plugins', // plugins
'org.codehaus.groovy.grails.orm.hibernate', // hibernate integration
'org.springframework',
'org.hibernate',
'net.sf.ehcache.hibernate'
warn 'org.mortbay.log'
}
myplugin.someproperty = 'foo'