Yes, you can use differential and single-ended at the same time. The AI Config function is used for this. You have a channel array and a Coupling & input config array. For example, if channel 0 is single-ended and channel 1 differential, then element 0 of the channel array will have channel 0 listed and element 1 will list channel 1. Element 0 of the coupling/config array will specify the single-ended you want to use and element 1 will specify differential.
The VI you posted has AI Acquire Waveforms which has a subVI called AI Waveform Scan. AI Waveform Scan has inputs for coupling & input config because AI Waveform Scan calls AI Config. You can modify AI Acquire Waveforms to pass in an array of channels and the input config array. Just be sure to give it a new name and save it to a new location. You could also just call AI Waveform Scan instead of AI Acquire Waveforms.