API Question. How to update *custom* lookup fields through the api

API Question. How to update *custom* lookup fields through the api

Hi there,
I am trying to insert/update records with the API, that include *custom* lookup fields.  
I've only been able to find how to edit the built in lookup fields via the api.
Can you please let me know how to edit the custom lookup fields through the api?
Thank you,
David