Yes you should be able to do that. look at the signal generation examples shipped with LabView
You can create a 2 D array, with each row representing a wave form per channel. The number of points of the wave form (per row of the 2 D array) represent the number of points in the output buffer
The wave forms can have different amplitudes/shapes, and therefore they are independent in this sense.
However, you need to set the update rate,which is the same for both channels. The update rate together with number of points per buffer determines the frequency of the wave forms. This means the two wave forms will have the same frequency.
To have different frequencies, you need to have say, on wave form with one cycle per buffer, and the other waveform have 2 cycles
per buffer. in a case like that the frequency of the second channels is twice that of the first channel, and so on
The two wave forms are then not truly independent, they may have different amplitudtes/shapes, but related in frequency.