For water survival training, do I use FM 3-22.20, chapter 13&15 or TC 21-21? FM 3-22.20 is superseded by FM 7-22 which doesn't mention it!?

Try Tc 21-21

I just went through a train the trainer course to instruct the CWST and we used TC 21-21.

This is a common occurrence as new manuals are released, overlapping and conflicting guidance or doctrine or holes
As you have identified the training is still required your choices are find an alternate document to bases the training off, or go backwards to the last manual that covered the training.

Personally Id revert to an older manual if nothing current is available ..as the training is not outdated, CWST is kind of basic and standard