In the longterm, is it better to work internally for a brand or work for an agency?
This depends a bit on the type of job you want. In general, agencies need flexible people, and great work for five brands shows a wider skill set than extensive work for just one.
How do I apply for a specific job when I don't know what, specifically, I want to do within an agency?
You don't. Do internships until you know. When you apply for a job, you need to believe in your heart that you want that job more than any other job in the world. (Or at least act like you do.)
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