Drupal site Phonegap application field collection
make sure a field collection exists if you want to go through the Field collection module. Then write the custom php code make sure to use the field collection api. here is an example. another example.

You will have to use AJAX from your phone gap app and send the data you are collecting to your server then use the drupal code to process and insert. 
AJAX from phonegap to PHP

Let me know if you need any more help, i'm just really busy as of late or I would provide a more detailed answer. It's difficult not having the code in front of me.