Answer: Annual plants have root systems that go about 12 inches deep. Since your box is only 6 inches deep, I'd suggest building it up somehow, or taking out the bottom and then digging/loosening the soil underneath it for at least 6 inches. Your goal is to have loose, arable soil that roots can easily penetrate.
Ants are good soil builders, aerating and decomposing organic matter, so I would let them remain.
Q&A Library Searching Tips