I'm working on a project that allows multiple users to submit large data files and perform operations on them. The "backend" which performs these operations is written in Perl while the "frontend" uses PHP to load HTML template files and determines which content to deliver. Data is stored in a database (MySQL, SQLite, Oracle) and while there is data which has not yet been acted upon, Perl adds it to a running queue which delivers data to other threads based on system load. In addition, there may be pre- and post-processing of the data before and after the main Perl script operates (the specifications are unclear) so I may want to allow these processors to be user-selectable plugins. I had been writing this project in a more procedural fashion but I am quickly realizing the benefit of separating concerns as to limit the scope one change has on the rest of the project.

I'm quite unexperienced with design patterns and am curious what the best way to proceed is. I've heard MVC thrown around quite a bit but I am unsure of how to apply it. Specifically, what are some good options to structure this code (in terms of design patterns and folder hierarchy)? How can I achieve this with both PHP and Perl while minimizing duplicated code between languages? Should I keep my PHP files in the top level so I don't have ugly paths in the URL?

Also, if I want to provide interchangeable databases, does each table need its own DAO implementation?