Currently I am designing few devices based on MOS6502/WDC65C02 CPUs.
I am going to use Motorola MC6840 timer circuit to generate interrupts and signals.
In particular I need:
1) Basic timer interrupt, to measure "system time". I'd like to implement something like millis() function from Arduino.
2) Square waves (without PWM, just standard 50% duty cycle) to generate basic audio "beeps" and to control stepper motors.
3) Pulse counting.

I've already read datasheet, but some things are still not clear to me.
1)I see there is no need to wire each timer input to system clock, if I want to use it to clock the timers. It could be distributed internally, from "E" pin. But what to do with unused timer inputs? Should I pull them up with resistors or simply left them disconnected?
2 Is it possible to use GATE input to "mute" its output, as it was done with Intel 8253 chip? If not, can I left unused GATE inputs disconnected or should I pull them up with resistors?

It would be helpful if you posted the datasheet or a link to it. This makes it a bit easier for anyone wishing to assist you.

Unused inputs should never be left unconnected with chips like this (MOS and CMOS). Tie them high or low, or used a resistor to pull them high or low.

cheers,
Jeff

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In 1988 my 65C02 got six new registers and 44 new full-speed instructions!
https://laughtonelectronics.com/Arcana/ ... mmary.html

As is typical of NMOS hardware from that time, it's kind of slow and a bit weak in the knees.

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x86?  We ain't got no x86.  We don't NEED no stinking x86!

You might want to look into the W65C22S which is rated for much higher speeds, and from what you've written about your requirements, it can do everything you need (plus more). It's in current production too, with no end in sight. OTOH, if you just have some 6840's and you just want to have fun with them, there's nothing wrong with that, either.

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http://WilsonMinesCo.com/ lots of 6502 resources
The "second front page" is http://wilsonminesco.com/links.html .
What's an additional VIA among friends, anyhow?