Or is it enough just to do this on the indexer? I'm in the midst of fine-tuning things, and it would be great if I could alter timing intervals and what is being monitored from just one place. I saw this question asked before, but the answer was painfully ambiguous.
Not sure which question/answer you are referring to.
You need to alter the interval and toggle enabled/disabled where ever the inputs are being collected, most likely on the forwarder.
Have you looked at the Splunk Deployment Server?
http://docs.splunk.com/Documentation/Splunk/5.0.3/Deploy/Aboutdeploymentserver