I put the tomato plants right into the empty peat pots. You can put a little dirt in the bottom if you want, either way should be fine. Right now I want to generate as many roots along the stem as possible and shorten the length of the stem. Shorter, more compact plants with more roots grow better than their long and legging counterparts. This is especially true if you are buying transplants from the store. Definitely avoid the leggy ones. (You can trench plant those if that's all the store has.)