I think the place you probably want to start is with the manual for the device itself - Agilent's manuals are usually pretty good about explaining the use of OPC, WAI, and SRQ's for controlling the device, and typically provide some HP-BASIC examples that would show you typically patterns of IO, including wait commands.
In general, straightforward configuration commands should not require waits between them - the device itself is going to buffer those commands and process them as it finishes prior operations. Where it becomes more important to get synchronization correct is first not taking measurements until the device's configuration is fully settled, and second in not trying to pull data from the device until the device is ready. For the first case you might use a WAI command, assuming that the device actually performs a wait on time-expensive configuration. For the second case, you might set the device to raise a service request when data is ready. Again, the instrument manual should explain exactly which bits in the status register you need to enable and query for in order to set up SRQ polling.