The answer to the below linked question is kind of the beginning to answer your question. You will need to do this with VBA, doing something like this:
Do While i <= cols
Do While j <= rows
//set conditional formatting for range ij:i(j+1)
j = j + 2
Loop
Loop
I'll see if I can create a specific script for you.
Format Top 3 and Bottom 3 Values for each row
EDIT:
I've tested this just a bit on a small data-set I created. It appears to work as requested. All you need to adjust is "cols" and "rows" to accurately represent your data-set.
EDIT2: Code has been slightly modified to fix a slight issue I found.
Sub Conditions()
Dim i As Integer, j As Integer, cols As Integer, rows As Integer
cols = 2
rows = 10
i = 1
j = 1
Do While i <= cols
Do While j <= rows
With Range(Cells(j, i), Cells(j + 1, i)).FormatConditions.Add(xlTop10)
.SetFirstPriority
.TopBottom = xlTop10Top
.Rank = 1
.Percent = False
With .Interior
.PatternColorIndex = xlAutomatic
.Color = RGB(0, 255, 0)
.TintAndShade = 0
End With
End With
j = j + 2
Loop
i = i + 1
j = 1
Loop
i = 1
j = 1
Do While i <= cols
Do While j <= rows
With Range(Cells(j, i), Cells(j + 1, i)).FormatConditions.Add(xlTop10)
.SetFirstPriority
.TopBottom = xlTop10Bottom
.Rank = 1
.Percent = False
With .Interior
.PatternColorIndex = xlAutomatic
.Color = RGB(255, 0, 0)
.TintAndShade = 0
End With
End With
j = j + 2
Loop
i = i + 1
j = 1
Loop
End Sub