1. If the instruments have a trigger mode, you should be able to have the instruments acquire simultaneously and then you will read sequentially. Your instrument manuals should have a description of what (if any) triggering modes they support.
2. In order for the FFT to determine frequency, you need to provide the sampling rate. If you create a waveform data type, you should be adding this info from either parameters you set in the program or from a setting in the instrument that you can read back and use.