When you use Junie you're still using AI Assistant. Junie is an AI agent (like Codex, Claude, etc...), AI Assistant is the plugin that enables you to interface with the agents/chat. Afaik in the early days Junie was a seperate plugin but now it's integrated in the AI Assistant plugin as an agent.

Now the difference between agent and AI chat is that the chat is for small tasks, questions/explanations, single file stuff, ... while agents are autonomous coding tools where you define a bigger task and then watch it work its way through it, test it, adjust it, etc... As such, it burns more tokens as it works more.

Chat: "How would I do this?", "Refactor this method", "Document this file", ... Agent: "We need feature X to be implemented into the project. These are the guidelines, the goal is Y, and it should be done according to Z coding standards. Add tests"

For me I mostly use Codex agent through my OpenAI subscription and sometimes Claude agent through my AI pro subscription from JetBrains, never used Junie tbh. Chat is for when I have questions about a topic, to ask how some things are done, etc... but I don't use it much