I think you may be getting a bit confused with what Information Architecture is as it isn't referred to as user flows.
The definition of Information Architecture as defined by usability.gov is the following:
Information architecture (IA) focuses on organizing, structuring, and labeling content in an effective and sustainable way. The goal is to help users find information and complete tasks.
In the context of your question, the Information Architecture wouldn't be specifically called out in a Customer Journey Map but the Information Architecture will influence how the Customer Journey plays out.
For example, "Joe navigated from the Home Page to the Products page as he was wishing to buy a jacket. He then clicked on the Jackets category to view the jackets available". In this instance the Information Architecture has been defined with the Products page being on Level 1, with the Jackets page being on Level 2. Though the Information Architecture isn't specifically called out in that Customer Journey explanation, it has influenced the Customer Journey for Joe.
In terms of finding good references for good IA (and how to design a good IA), this Smashing Magazine article is pretty good. It explains what Information Architecture is, How to avoid pitfalls of bad IA and how Card Sorting can be used to design a good Information Architecture.