It's my understanding that when a Timer is used on an Arduino (in my case the Arduino Mega), it can disable analog write on some PWM pins, which pins depends on the Timer being used. For instance on the Mega, pins 44,45,46 are controlled by Timer 5. 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.
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().
When using an timer (other than by PWM) you can choose to enable it's output to a pin (which basically is what PWM does). So you can still use them as a digital pin (if you choose not to).
You could set up an PWM signal and enable timer interrupts afaik. But changing PWM, would also change the timer.
There is a difference in only using Arduino functions, or changing the registers directly. Try to read the "timers" part of the datasheet and find some tutorials about avr/atmel/atmega register changing or/and setting up timers.