I recently germinated and planted lemon seeds. So far they have sprouted and are healthy. My concern is, I planted about 2-3 seeds per container, and now I have about 2 sprouts in each container. When I need to transplant them, do I need to separate the sprouts and plant them individually? Or can I leave them together? Will it be two trees in one pot eventually? Or turn to one tree?
They need to be potted separately, if you mean you planted citrus lemon tree seeds. You can move them into small, separate pots as soon as each seedling has two sets of true leaves (the first leaves are cotyledons, and don't count as true leaves).
You don't say where you got the seeds from - if they are just seeds from a lemon fruit you had, the resulting tree and its fruits will likely be different from the original lemon you bought.