The amoeba issue is exceedingly rare. AFAIK there were only two separate Lousiana cases EVER that seemed to have gotten infected with the amoeba from treated tapwater nasal irrigation, however tests of their water supplies showed no contamination so it's unclear how the amoeba got into their water. Using untreated water, like from a well, is probably not a good idea.

I have used a Neti pot once or twice a day for years. It's as second nature as brushing my teeth now. To rehydrate dry nasal passages and clear out mucuous, an isotonic solution is very soothing. It's a bit uncomfortable, but the literature indicates a hypertonic solution is best at stimulating the tiny hairs that line the mucous membranes, to maintain a healthy barrier against bugs. Definitely a plus during cold and flu season. For routine use, I try to use a hypertonic solution.