How do I connect a pin that is not included on the main symbol or any of the gates of an Eagle part?
Sounds like the parts are not defined exactly as you would like them in the Eagle library.  I would make new versions of the parts in the library (I don't suggest directly editing the existing ones) by copying the parts and adding the missing pins.  In the case of the HTSSOP package you will also want to add the thermal pad for the layout.

There are several tutorials on the web re creating and copying parts in the Eagle library, such as this one.