Do I just manually inputting the frequency you want using a square wave when use PEMF Coil?

Yes, you can run a frequency set, a single frequency of choice, etc...

There is a shell preset for PEMF Coil in Presets tab.

Also, operation would be not much different than when using Spooky2 to drive a remote.

One can even just use the JW - Healing (Remote) preset and change the amplitude to 20. Then load frequencies of choice and stop when done.

If you have a particular frequency in mind, you can crate a custom frequency set to load. Use the File, Create Frequency Set to do this. The August software and above has Spooky Coil (XM Direct) - JW preset, you can directly use it.

To use the PEFM coil, either plug it directly into Out 1, or use a barrel connector to attach to the MN or BN port of the Boost 2.0.

Do not use the CS port.

If you have a boost 1.0 cable, you can forgo the barrel connector.
Use a square wave to start, either with or without offsets.

Please check this blog:
How to Connect PEMF Coil to the XM Generator
http://www.spooky2-mall.com/blog/connecting-pemf-coil-to-the-xm-generator/

Choice of frequency is up to you. Anywhere from .00001 Hz to 20 MHz.

For more details, please check:
https://www.facebook.com/groups/spooky2/permalink/588240698004504/