I don't know really how they detect when EA is used. I can imagine that the Magic Number tells that, which is 0 for all manually created trades and orders, so when it is different than 0 it means that some EA created those trades/orders. In the EA you can choose to create trades/orders with Magic Number 0 (go to Options -> Project Options and set Magic Start Number to 0), but I guess there is something more than that, maybe some hidden information is sent with the trade/order which tells whether EA is used or not. Again, I don't know for sure.
J