Brian,
in PDMLink Site administration UI there is a link for Worker Agent Administration.
You need to click the "configure" link in that toll and click the "Edit" button.
Select your APE worker from the list of configured workers.
Clicking through a few pages you get to the page where you see a textbox "Worker Instances". Just enter the appropriate number here, save and reload the agent configuration file.
What I do not remember from the top of my head though is how PDMLink / APE publishing behaves as to when jobs are removed from the queue. You might also need to add Publising queues for each worker instance you add to get real parallel processing.
You should use Windchill HelpCenter to lookup how to add Publishing Queues.
Hope that helps.
Sirko