I would normally recommend including the properties files in the EAR file unless you need to change a file and don't want the hassle of rebuilding and redeploying the EAR. This could apply to a logger or configuration file. (Having said that, it may be possible to deploy an exploded directory - as you can with WebLogic Server - in which case you can edit the properties file in situ.)
There are several ways of achieving this. One way is place your JAR file containing the properties files anywhere in the EAR (say the root) and refer to it in the Manifest Class-Path of the J2EE modules that need access.