Spent most of the day reading through http://pkp.sfu.ca/ojs/docs/technicalreference/2.1/ in particular the sections on Plugins to try and figure out to what degree the changes I have to make can be accomplished through plug-ins. Not sure yet whether the event handling infrastructure will allow me to modify the GUI elements (e.g. in the Manager/Setup area and in the Author/Submission/NewSubmission area. Also spent a bit of time looking through the Smarty documentation at http://www.smarty.net/docs/en/ . I don't think I'll need to know very advanced stuff for that, other than possibly how to implement conditional blocks based on php variables set elsewhere (namely in the code I add).

I may try creating an absurdly simple plugin that simply plunks some content into the appropriate place in the appropriate template file (i.e. rather than me modifying the file in the base code) as a start.