Quadrature encoder and loop count

After much our spend it work in interrupt's like Henrik suggest me and I am nearly finish.
Need only one sugget more from peoples here.
Next problem or maybe not :?
QEI counter count in circles up/down for example 0-1999 and oposite 1999-0...in 4X mode.
Now when I am at position 100 for example and command new position - 100 pulses motor will go to 0 and stop - OK but if maybe inertia of shaft move QEI only one step down then here is problem Setpoint is on position 0 value but QEI is 1999!
I am little confused on how to set relation between Setpoint and QEI register of position ?
I want to move motor to any direction with PID without limit of numbers of turn to+ or minus.
Maybe I ned dead zero like minus limit /?
Any suggest.
Regards Robert:)

Here is QEI module count set to count from 0 - 999 .
x is number of cyrcle's of QEI module up and down.
QEI variable is final counter..etc

Code:

---

loop:
    z = 0
    PosHigh = POSCNTH                          'Get high byte of counter
    PosLow = POSCNTL                            'Get low byte of counter
    PosTemp = POSCNTL                          'Get low byte again 
    If PosLow - PosTemp = 0 then Goto Done      'Compare, if equal we're done.
    PosHigh = POSCNTH                          'If not, get values again.
    PosLow = POSCNTL
    z = 1
Done:
    Position = POSHIGH * 256 + PosLow          'Put high and lowbyte together.
    if position > 1000 then position = 1000
    if position < 1 then position = 0
    h = QEICON.5                                'QEICON.5 for right = 1 for left = 0
    if PIR3.2 = 1 and h =1 then x = x+ 1
    if x <> 0 and PIR3.2 = 1 and h =0 then x = x- 1
    PIR3.2 = 0                                  'PIR3.2 maxcount transition down or up was detected
    h = 0 
    QEI =  (1000 * x) + position                    ' increment  total counter
    if z = 1 and h = 0 then QEI = QEI -(1000-position) ' dectement  total counter
    if h = 1 and QEI = 0 then
    QEI = 65535
    endif
    if QEI > 65535 then
    x = 0
    QEI = 0
    endif
    if porta.0 = 0 then setpoint = setpoint + 1
    if setpoint > 65535 then
    setpoint = 0 and QEI = 0 and x = 0
    endif

---

Butwhen I count to minus after QEI variable com to 0 if I move shaft of motor more to CCW real QEI conter will continue 999,998 and if my setpoint stay at 0 I am in big problem...
Any suggest please
Regards Robert