Mount Sahrotaar and fly to the tower where Miraak lives. Note that on your way you can eliminate a few Seekers on one of the islands - it's however not required. Surely you have noticed that the dragon follows a predetermined path, so sooner or later you will reach your nemesis. Your arrival will surprise him, giving you the chance of dealing the first blow.
The fight will follow a patter - when Miraak's health falls down to a certain level (around 30%), he will teleport to an inaccessible point on the map and drain the soul of one of the nearby Dragons (therefore curing his wounds). The process will repeat four times - the last one to die will be Sahrotaar, who might try to attack you before that (using Bend Will again will kill him).
The tactic against Miraak is quite easy - stay as close to him as possible and attack in close combat (he's far more dangerous during a ranged fight). The enemy can use multiple spells - especially electricity - but isn't great in a normal fight. IF only you have a couple healing potions and are able to fight, you should be fine.
When Miraak is left with very little health and there are no more Dragons in the area, Hermaeus Mora will appear and kill him. That way the main story of Dragonborn will come to an end. Before leaving the unfriendly land of Apocrypha, search the enemy's body and use the book in the middle of the room for an additional prize. You will be able to use the obtained dragon souls (11 in total) to get back badly distributed skill points. This very handy option can be used as many times as you like (by returning to the location).