How can one use Sweave and similar tools with AMC? Is there a preferred workflow?
I'm not sure I know how sweave works, but if it is some kind of preprocessor which produces a LaTeX file, you should be able to feed AMC with this LaTeX file (and possible extra files as images or so).
If you need AMC to call this preprocessing for you each time you click on "update the documents", you have to build your own "filter" and add it to AMC (as a plugin). This requires a little perl knowledge.