I switch nostrils half-way through the process each time. (I do half a pot in one nostril, half a pot in the other.)

I read a study this spring that suggested that neti pots may increase your susceptibility to airport and respiratory illnesses because a certain amount of mucous in the sinuses acts as a first layer of defense, trapping incoming microbes before they can get anywhere harmful. Thinking back, I actually did get sick a lot more, and had some severe respiratory illnesses, during using my neti pot. The study suggested that using neti pots is still good as a symptomatic treatment used when things are bad -- during the worst of allergies or when you're sick and super congested -- but that you shouldn't just use it every day.

Since then I've stopped using it every day as a matter of course, but I keep it around to use when I feel that I need it. The incidence of my getting ill has, in fact, decreased.

Now, this is all EXTREMELY un-scientific and anecdotal, so you shouldn't take my experiences as proof, but I've decided to change how I use it.