Here's a writeup on the actual process:
http://www.q45.org/plenum.html
At some time soon, your fuel, vacuum and/or coolant hoses under the plenum will deteriorate to the point that they'll start leaking. The knock sensors are also probably not functional anymore, either. To get to either, the plenum has to come off - something you probably don't want to do more than once. So, it's economical to deal with everything under the plenum at once.
The valve covers can be done separately, but there isn't much additional labor to do them when you do the under-plenum work, too.