If the Dragonborn is returning to Blackreach, the Great Lift at Raldbthar is the entry point closest to the Tower.
The tower is located in the south-southwest corner of Blackreach. Blackreach can be found by traveling through Alftand, Mzinchaleft or Raldbthar of the major Dwemer ruins, but the quest marker will always direct the Dragonborn to Alftand. It is also possible to access it by forcing a plate against the wall and sprinting into it.
The only way to do this is to have started the quest, "Discerning the Transmundane." Septimus Signus' Attunement Sphere is required to activate a Dwarven mechanism opening a door to Blackreach. To reach the other side, Blackreach must first be traversed.