I’ve seen AppleScript solutions for grabbing the file path and using it to save the output files, which you can add to the Automator workflow: https://stackoverflow.com/questions/24087228/mac-automator-combine-pdf-files-save-in-same-folder
You could also select Options under the Move Finder Items and check “Show this action when the workflow runs” to get a prompt for you to chose the output path.
If you happen to have Alfred, there is a great workflow called Alfred PDF Tools which makes merging PDFs (and splitting, etc) super easy: https://www.alfredforum.com/topic/9276-alfred-pdf-tools-–-optimize-encrypt-and-manipulate-pdf-files/