There is a specification for which bus you're communicating over and you have to use it. Otherwise, all commands will go out over the first card. Also, with two cards, you only have to have unique addresses on each bus. For VISA, which I recomend you use, the resource name takes the form of GPIBx::ADDDR:INSTR so you would GPIB0:: for instruments connected to the first boards and GPIB1:: for instruments to the second. VISA is really a lot easier because you can just select from a list of available instruments. For traditional GPIB, to quote the on-line help "When there are multiple GPIB Controllers that LabVIEW can use, a prefix to address string in the form ID:address (or ID: if no address is necessary) determines the Controller that a specific function uses. If a Controller ID is not present, the functions assume Controller (or bus) 0."