Plugboards are only activated when you "Send to a device" Or "Save to Disk." But you can further narrow that even, by having your plugboard only affect a specific format (epub, mobi) and/or a specific device. You'll never see the modified metadata within calibre... only on the device/app you're sending/saving to.
In the 'add new plugboard' row; Choose your format and choose your device (you could choose 'any' for both just to get started... but you may want to be more selective if you deal with many different devices and formats). In the top 'Source template' field enter:
Code:
{series_index:0>3s} - {series} - {title}
In the top 'Destination field' select 'title' and click save plugboard. Close calibre Preferences.
Now send a book (that already has series metadata configured in calibre, of course) to your device and see the results (you may have to change the destination field to 'title_sort' depending on what metadata field your device uses to display titles).
The above template will cause the title to appear as:
001 - Series Name - Book Title
Highlight the saved plugboard in the 'Existing plugboards' box and you'll be able to tweak the source template to show whatever you want.
So basically you're creating a template to combine existing metadata fields and then jamming that combined data into a different metadata field... but only when you send the book to a device or save to disk (depending on how specific you've gotten).
Hope something there helps.