Hi,

If we look the datasheet for the PIC18F886 you will notice that we have 3 timers:

Timer0: 8-bit Timer/Counter with 8-bit
Programmable Prescaler
• Enhanced Timer1:
- 16-bit timer/counter with prescaler
- External Gate Input mode
- Dedicated low-power 32 kHz oscillator
• Timer2: 8-bit Timer/Counter with 8-bit Period
Register, Prescaler and Postscaler

Timer0 can be clocked with the T0CKI (RA4)
Timer1 can be clocked with the T1CKI (RC0)
Timer2 can NOT be clocked with an external pin.

There is an other possibility and that is that you use interrupts for counting but that might upset the serial data unless you also do that part interrupt based.

But since you say that you are new to pics I would suggest that you use the timers as counters. Associated with the timers are the timer registers and that is where the current number of counts are stored.

8-bit timer/counter register (TMR0) for Timer0
16-bit timer/counter register pair (TMR1H:TMR1L) for Timer1

I suggest you start with Timer0 since that is the easiest one to set up.
5.0 TIMER0 MODULE in the datasheet is something you must read and understand before you will be successful with this.