Hi Sripad,
The two functions are essentially the same--it is just dependent upon what kind of data you want to write. As far as timing, they're likely within clock cyles of each other. What is going to slow down your operation is the fact that your USB-6008 uses software timing. This means that everytime you need to write, it is dependent upon the state of your system. If your system is doing a lot of processing at one moment, it will take longer than when it is doing less processing. This means your pulses will not be evenly spaced. This software timing is what is also going to either make or break your ability to get your pulses at 10-15 fps.
More information about each function:
DAQmxWriteDigitalU8 writes multiple 8-bit unsigned integer samples to a task that contains one or more digital output channels. Use this format for devices with up to 8 lines per port.
DAQmxWriteDigitalLines writes multiple samples to each digital line in a task. When you create your write array, each sample per channel must contain the number of bytes returned by the DAQmx_Write_DigitalLines_BytesPerChan property.
