You typically would want to do this on the Form level (users should NEVER have direct access to the tables - all manual data entry should be controlled through Forms).
On your Form, you can use the BeforeUpdate event of the Form to check and pad the leading zeroes for that field.
For example, the code might look something like this:
Code:
Private Sub Form_BeforeUpdate(Cancel As Integer)
Dim curEntry As String
curEntry = Me.FieldName
If Len(curEntry) < 6 Then
Me.FieldName = Right("000000" & curEntry, 6)
End If
End Sub