One of my friends who was traveling with me took Paludrine and he had little to no side-effects. Although I only had to take Nivaquine twice a week versus twice a day of the Paludrine variety, it would have been more pleasant to have less side-effects. But I would consult your doctor to find out what is the best for you to take. In addition, drinking Eau Vive or mineral water helps. We bought a few bottles of Eau Vive to start with and then we boiled water to save money.
Iodine tablets help, too.
Eating safely is a good suggestion. Most diarrhoea is contracted through eating inadequately heated, contaminated food, salads, ice, icecream, etc. I was an adventurous eater during my stay in Madagascar. And it was NOT a pleasant experience. Buy icecream in cities such as Tana, Toliara, and Diego Suerez.