The Well of Souls comes with two abilities eligible for upgrades on the battlefield: Sink Deeper and Roiling Revenants. Sink Deeper is available from the Level 1 card and increases soul capacity (each soul adds 10 damage to Well of Souls damage). Roiling Revenants is available from the Level 1 card also and lowers attack rate by 0.1 seconds.
As the Well of Souls upgrades, more upgrades will be available for both abilities. Sink Deeper can be upgraded a total of 4 times, and Roiling Revenants 3 times as at level 7.
To use the Well of Souls most effectively, it should be placed in important cross-sections on the map where several mobs collide. Slowdown Towers posted around this tower helps crowd the enemies into a group, making it easier for the Well of Souls to hit swarms at once.
Because the Well of Souls becomes stronger with each kill, in the early stages of the battle the player should not rely too heavily on it. Upgrading Sink Deeper allows for more souls to be swallowed, thus increasing its Magic Attack as the battle progresses. Upgrading Roiling Revenants in early stage of the match should be avoided because the slight difference won't be worth the high cost. Also, if possible, try feeding kills to it early on by not building as many towers, or positioning it at an earlier cross-section. This will allow it to reach maximum strength earlier on in the level so that it can help you out in the later waves. Otherwise, the tower may have difficulty getting any kills, preventing it from ever reaching its full potential.