I.
a - There can be multiple outputs.conf in a splunk installation for eg: etc/local, etc/default,etc/apps/default,etc/apps/local etc. Splunk merges all the configuration files and applies it. If there are similar stanzas in two different configuration files, Splunk picks up the configuration based on precedence which is described here http://docs.splunk.com/Documentation/Splunk/6.4.2/Admin/Wheretofindtheconfigurationfiles#How_Splunk_determines_precedence_order
b - It depends on your installation. If you have a deployment server configured, it can act as a central server to deploy the configurations. More details : http://docs.splunk.com/Documentation/Splunk/6.4.2/Updating/Aboutdeploymentserver
II. You can route and filter data using props and transforms . Reference : http://docs.splunk.com/Documentation/Splunk/6.4.2/Forwarding/Routeandfilterdatad
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