Hi Hideya
You will not be able to do your application using the user defined waveform to generate your frequencies.
The user defined waveform memory is not generated as it is using an arbitrary waveform generator. The function generator uses a technology called Direct Digital synthesis (DDS) as most function generators use today. This method uses a constant sample rate, 100 MSps for the NI 5406. The various frequencies that the module generates is done by varying the number of samples per cycle of the signal going the DAC. This is done by selectively choosing specific samples from the look up memory. If you want a 10 MHz sine wave, the DDS only chooses 10 samples from the look up memory to generate the sine wave. The 10 is determined by dividing the sample rate (100 MSps) by the sine frequency (10 MHz). So, most of the user look up memory is not generated.
So, even if you created your own waveform which would theoretically contain the two frequencies, you would not see this at the output of a DDS function generator.
For more information of DDS, here is a pretty good and short description from Analog Devices:
Depending on the length of your sweep and the frequencies, a full arbitrary waveform generator (AWG) may be your only solution to have frequency steps less than 1 ms. The amount of memory on the module will be important on whether the waveform will fit in an AWG’s memory.
Jerry