For optimal hamstrikg stretching, use the contract/relax method. Using your legs when lifting is excellent to prevent further injury to your back. Working on your back seems of the utmost priority. Pilates usually focuses on core training, which is optimal. Stretching and mobility training for your spine might also be advocable. As with all these things, it is hard to give advice without being present oneself in order to examine, evaluate, and adjust based on what happens when advice is followed. Checking with your Pilates instructor is a very good idea since that person would be able to suggest and demonstrate specific excercises and follow up on your progress.