I usually plant 3-5 seeds per cell with my tomatoes. When the seedlings are a few inches high you can separate them into their own cells or larger containers. I wouldn't be too worried about damaging the roots, tomatoes are usually pretty resilient. You can pop the seedlings out of their cell along with the soil using a spoon then gently pull the plants apart and replant them. Try not to squeeze the stems too much. Even if you loose some you'll still have more than If you were to just thin them out. Sometimes I don't get around to separating them until I plant them in the garden, which I don't recommend. They still grow fine, but they seem to take a little longer to bounce back from the transplant shock. When you do start putting them outside be careful of sun scald. Start with a little time outside then increase it over 4-5 days. Like smallaxe said when you transplant them in the garden use compost and bury them to the first leaves, tomatoes can sprout roots all along their stems. Great project to do with your 4 year old. Have fun and good luck.