As you move the AN0 samples, move the AN1 samples the same way...
Code:
SAMPLE_AN0 WORD [12]
SAMPLE_AN1 WORD [12]
CounterA var BYTE
DataTemp var WORD
Getsamples:
 For A = 1 to 12
  adcin 0 SAMPLE_AN0[A]
  adcin 1 SAMPLE_AN1[A]
 NEXT A
Sortdata: 'THIS WILL SORT SAMPLES_AN0
CounterA=0
SortArrayLoop:
If SAMP_AN0[CounterA+1] < SAMP_AN0[CounterA] then
    DataTemp = SAMP_AN0[CounterA]
    SAMP_AN0[CounterA] = SAMP_AN0[CounterA+1]
    SAMP_AN0[CounterA+1]= DataTemp
    DataTemp = SAMP_AN1[CounterA]
    SAMP_AN1[CounterA] = SAMP_AN1[CounterA+1]
    SAMP_AN1[CounterA+1]= DataTemp
If CounterA > 0 then CounterA = CounterA - 2
    endif
    CounterA = CounterA + 1
If CounterA < 11 then goto SortArrayLoop
END