Try something along the lines of...
set theWorkflowName to "Merge PDF Files"
tell application "Automator"
set myWorkflow to make new workflow with properties {name:theWorkflowName, path:POSIX path of ((path to desktop folder as string) & theWorkflowName & ".workflow" as string)}
save myWorkflow
add (first Automator action where its id = "com.apple.Automator.SpecifiedFiles") to myWorkflow
end tell
I think the key is to create the workflow, then save it, and then add the action.
Hope this helps!
-Ben