When should I use the PEMF, ultrasound or other modes of transmission?

It will be better to use contact mode together with the plasma tube.
The modified contact of Spooky2 Central does not kill anything directly. The TENS pads from the Spooky2 Central runs at a fixed 100 Hz. The output is a 320v half a millisecond pulse. The effect is to induce electroporation, the momentary reversal of the electrical charge of our cell walls. This makes the cells more permeable, allowing the plasma to penetrate deeper to get at pathogens that hide deep inside.

To use this in conjunction with the plasma output is a good idea. The generator is not capable of doing this.

There are 3 different frequencies in Spooky2 Central. One is a fixed 100HZ, that is for both contact and coil.

The Ultrasonic is the second frequency. It is either 1/16 or 1/256 of the frequencies applied for Spooky Plasma. Spooky2 Plasma frequency is whatever you choose.

You can check below link to learn more detailed:
http://www.spooky2support.com/hc/en-us/articles/217625397
http://www.spooky2support.com/hc/en-us/articles/218023498