Personally, if you really want them I wouldn't rely on getting them on check-in. If you want to gamble, check in as early as possible... If he is young and you are at the desk an airline will usually try to accommodate you to sit together but they are not necessarily going to give you window seats or have window seats to assign you. What sort of plane is it and who is flying it? Chances are load factors are around the 80% mark. It is probably either configured in a 2-4-2 or a 3-3-3 configuration. Looking at the load factor and the configuration and work out the chance of two seats free. pairs of seats fill up faster and people prefer either aisle or window so you have to decide if the load factor is low enough to risk it.