A common garden rule is never to install plants below soil grade. Often plants will languish, and possibly die, if planted too deeply. However, this is not the case with tomatoes. The stems of tomato plants have the ability to develop roots when set underground. The increased root system gives the plant a stronger base and increased access to water and nutrients. Plant your tomatoes as deep as possible, leaving three to four sets of leaves above the soil line. Pinch any flowers that will be below grade. A plant that is 12 inches tall can be planted 6-8 inches deep. In heavy soils, where deep planting is not possible, use a trench system. Instead of digging a deep hole for the tomato plant, dig a long trench. Set the stem on its side in the trench. Do not plant on hard, compacted soil which will prevent new roots from penetrating the soil and growing.