Custom Instructions in the ChatGPT UI allow you to provide guidance on how the model should behave for a particular conversation. It's a way to fine-tune the interaction without needing to modify the underlying code or model.

In the Chat Completions API, you can achieve a similar effect using system messages. So system messages can be used to instruct the model how to behave in a conversation, such as adopting a specific tone or following particular guidelines.

Ultimately both techniques aim to provide a way to guide the model's responses in a conversation, but they are used in different contexts (UI for Custom Instructions, API for system messages). So if you're using the API you should be using the system messages from the Chat Completions API.

In other words, system messages are to our API as custom instructions are to ChatGPT in the UI and custom instructions don’t offer additional token savings.