Automator is incredibly powerful, but at the same time the most useless and semi-functional piece software I've ever encountered. I recently built my first Automator Workflow to watermark a PDF. I wanted to load selected PDFs from the Finder, and for each PDF create a file in the same directory with a -watermark suffix appended. file1.pdf and file2.pdf would yield file1-watermark.pdf and file2-watermark.pdf.
It took me much too long to figure out that it wasn't easy (or maybe even possible) with Automator, even though it's simple to do from the command line.
Each Automator action returns a result. That result is passed to the next item in the chain, assuming the item is accepting input. The key is to chain a series of Get Value of Variable calls together, which are passed to a shell script as
$1-$n and the special
$@ variable. I've written a short primer on using Arrays in Bash that may be helpful.
A crappy picture is worth at least 68 words, so here is what a sample workflow looks like:
You can download the sample workflow here.
If you want to loop through selected Finder items one-at-a-time, the best way is to use Nyhthawk Productions's excellent Dispense Items Incrementally action.