In Excel VBA, use a Dictionary. Use your items from one of the sheets as keys, QTY as values. Put the item/QTY pairs of sheet 1 into the dictionary, then run through the items of sheet 2 update the dictionary accordingly to get the differences in there. Finally, put the result into sheet 3.
EDIT: here is a complete example in code (you have to set a reference to the Microsoft Scripting runtime to get it working this way):
Option Explicit
Sub CreateDiff()
Dim dict As New Dictionary
Dim sh1 As Worksheet, sh2 As Worksheet, sh3 As Worksheet
Dim i As Long, v As String
Set sh1 = ThisWorkbook.Sheets("Sheet1")
Set sh2 = ThisWorkbook.Sheets("Sheet2")
Set sh3 = ThisWorkbook.Sheets("Sheet3")
For i = 2 To sh1.Cells.SpecialCells(xlCellTypeLastCell).Row
v = Trim(sh1.Cells(i, 1).Value)
dict(v) = -sh1.Cells(i, 2).Value
Next
For i = 2 To sh2.Cells.SpecialCells(xlCellTypeLastCell).Row
v = Trim(sh2.Cells(i, 1).Value)
If dict.Exists(v) Then
dict(v) = dict(v) + sh2.Cells(i, 2).Value
Else
dict(v) = sh2.Cells(i, 2).Value
End If
Next
For i = 0 To dict.Count - 1
v = dict.Keys(i)
sh3.Cells(i + 2, 1) = v
sh3.Cells(i + 2, 2) = dict(v)
Next
End Sub