If a Timer is used, disabling some PWM pins, can I still use those pins for Digital write?
If I enable Timer 5, does that mean that I can't use these pins for anything else? Or does it only mean I can't use those pins for AnalogWrite, and that I can still use those pins for DigitalWrite.


You can view the connection between the Timer and the pins as programmable. The connection is enabled by, for instance, analogWrite(). The Timer control registers have a setting for both the connection and control logic of the pin (clean, set or toggle on timer value match). 

You can use the Timer to generate interrupts without connecting a pin. This is the case with micros() and millis() which get their values from a counter which is updated by an ISR on Timer 0 (overflow). analogWrite() on pin 5 and 6 connects to Timer 0 value match logic. 

analogWrite() uses the Timer value match and connects the pins. Enabling only the Timer (as you suggest) will allow you to use the pins with digitalWrite(). You can also use the Timer ISR for overflow. The Timer prescale is set for analogWrite(). 

Cheers!