Elkwin Logstash uses <inst.dir>/logstash/logstash.conf as the configuration file. If you want to arrange your Logstash configuration as multiple files, you can create a directory with the same name and copy your files into it. Keep in mind that they will be processed in alphabetical order and a kind of numbering/sorting mechanism can be necessary.
You can use Logstash plugin-manager to install/manage plugins:
SET JAVA_HOME=<Elkwin inst.dir>\java
CD <Elkwin inst.dir>\logstash
bin\logstash-plugin.bat install <plugin-name>
More information about plugin-manager can be found here.