Hi Gerard,
Moodledata is the location for all data files used by Moodle (e.g. uploaded files, temporary caches, downloaded translations, etc.).
Any PHP files that need to be executed should be located within the Moodle code directory, or one of the subdirectories (i.e. the same place you find config.php and the mod/, lib/, admin/, etc. subdirectories).
If you explain a bit more about what you are trying to do, then it might be possible to suggest the best place to put the file within the subdirectories there (there are a range of different plugin types - report plugins would probably be the first one to look at).