If you want to minimize the application - just press the minimize button!

For what do you need the additional button? 
Do you know about the feature of calling an external application (e.g. for incoming call)? Take a look at the options menu.

PhonerLite is just a hobby project - designed to fulfill my personal requirements. I just share that for others.
I think for you it would be better to use a professional solution if you need such professional features. I can't offer it for you. Sorry.

If you press the X button you should see a warning dialog that the application will be closed and no incoming calls are possible anymore. So you can't PhonerLite accidentally. Maybe you have disabled the warning dialog...