I'm really confused by what you are doing.
To measure frequency with TMR1 you need to do this:
1. configure TMR1 to count external pulses on the input pin.
2. configure TMR0 as a timebase, the 'window' during which pulses are counted.
3. configure interrupts so TMR0 (and if necessary, the prescaler) generate regular timed interrupts.
4. In the ISR, read TMR1, this is your frequency, reset it to zero and if necessary reload TMR0 to get the right period (1mS).
If you do that, you will get a direct frequency measurement with no adding or subtracting needed. It will update every time TMR0 generates an interrupt.
Brian.