Your 2IC follows your overall strategy when selecting numbers and types of ships. See how strategy affects ship construction for more information.
To change your strategy at any time, just click on the "Change Strategy" button at the bottom of the 2IC Help screen for building ships.
You will now see a dialog box like this:
Just select a different strategy, and click on the "OK" button.
Changing strategy affects every aspect of what your 2IC does, not just ship building. Read the overview of strategies if you are in doubt about the effects a change will have.