“The Commerce Department’s Bureau of Economic Analysis (BEA) is the government agency responsible for measuring the balance of trade. According to the BEA, in 2008 the trade deficit measured approximately $696 billion. This total trade deficit was composed of an $840 billion trade in goods deficit combined with a $144 billion trade in services surplus.”
I heard somewhere else that the $696 figure comes from approximately 1.8 trillion in exports minus about 2.5 trillion in imports.
As it explains, since 1993 merchandise and services are combined into the trade deficit or surplus, which is calculated as exports minus imports. So the two calculation you refer to give the same result.