Where to use the php functions when adding fields to existing nodes?
Fields are attached to Entities, not Nodes. So the field is either attached to bundle that is your node (for all nodes, pre-existing or not), or it hasnt been attached to that bundle yet.

You can use field_info_field and look at the element bundles to see if your given field is attached to the given Entity. If it isn't you can use field_create_instance to add the field to your entity.

You can get a list of all entity types and inspect their bundle types with the bundles key returned from entity_get_info by calling $site_entity_list = entity_get_info(NULL).

Entities and fields are cached, so be sure you use something like drush cc all to be sure you're looking at up-to-date values for all these function calls.

EDIT:
You use these functions and PHP from essentially a small php script. Such business logic could be in a small module with hook_update_n() for instance. Or, you could use Drush and write a very simple PHP snippet using hte above 3 functions and some loops and call it using drush like:
drush php-script your-script-filename.php