1) Turn on Metadata extraction in CP, if you haven't already.
2) Turn on the 'Extract metadata from file name' settings and set up a regular expression for extracting the Well information from your file names. If you need help with this, I'd read the CP help on it or search the forum for other examples; I also like this online tool as a way to test out different regular expressions to make sure they work.
3) Make a CSV (in Excel or some other program like that) matching the well information to the triplicate information- it'll look a bit like this:
4) Click "Add another extraction method" in the Metadata module and hit "Import from file", then load your CSV.
5) When it asks you how to associate the file with your images, tell it the "Well" metatdata you extracted from the file name should be the same as the "Well" metadata in the CSV.