I've built a crud-based PHP API and I'd like to do some unit testing with it but I'm not sure exactly the best way to implement it.

The API has a few layers:

Code:
index.php
  You POST your API call to this page
api
  index.php sets up the autoloader/error handlers and sends the request here
database
  Class that interacts with a mysql database
crud
  Class that provides a few functions like create, read, update, and delete
myclass extends crud
  Just a sample class
Now, when I'm doing unit testing, I see two options:
  1. Test my API by using the api entry point at index.php. This means I would test the entire API by just sending requests to index.php and looking at the response I get back and checking to see if it's what I expect. This means I would never instantiate crud or database or anything on my own.
  2. Test my API class by class. If I want to test and see how my crud class is working, I would call methods on crud directly.


I can see pros and cons to each method so I'm not sure what's best. I feel like the second option is better because my tests are more isolated and thus a bug in the way I'm returning data from the API won't break a test on a function that fetches something from the database. The only issue I can see is that I will lose stuff like my autoloader so I feel like I'll be rigging my tests to make them work because they are connecting to classes in a way that the API wasn't designed to allow.