Hi Gerard,
Once you install Moodle, basically you have:
1. The Moodle Installation Directory, by default named "moodle" and usually created under the Document Root Directory (e.g. /some/path/public_html/moodle). In this directory resides all the Moodle code (php scripts, plugins, themes, etc.), and here is where you would put your own PHP scripts.
2. The Moodle Data Directory, by default named "moodledata". This directory has to be created outside of the Document Root Directory (e.g. /some/path/moodledata); this is so it isn't accessible via Internet because here are kept all the course content (PDF, videos, SCORM files, etc.) and student files (profile pictures, assignments uploaded, private files, etc.).
3. The Moodle Database, which can be MySQL, MSSQL, etc.
If you want to develop code to integrate it into Moodle:
1. You definitely need to get familiar with the Moodle structure and code (see: main page, developer documentation).
2. It would also be best for you to post at the General developer forum.
3. You could try and get a friend to help you with the project you have.
Cheers!