I use the waterplant baskets - the ones with the sides that allows the exchange of water. The waterlilies are planted in gravel with egg rock on the top so my fish cannot uproot the plants. DH put 'handles' of coated bellwire on the sides so that the pots of waterlilies can be removed from the pond without having to get into the pond.
I also like to use the once a year fertilizer stakes. I know if I had to fertilize the waterlilies monthly or every other month - they would be fertilized each spring - March/April and then probably not again. This works well for me as my understanding is that waterlilies are heavy feeders.
Jonathan - I was wondering if any of your waterlilies are fragrant?