If you are driving there on your own, it's very simple, just drive direction İzmir from Çanakkale, the signs on the road will lead you to Bergama no matter what! If you choose to use public transportation 'Otogar' is the word to learn. Otogar means 'intercity bus terminal'.
Assuming you are starting from Assos, Behramkale; you have two choices. You either get to Ayvacık Otogar or to Küçükkuyu Otogar, as Küçükkuyu is located on the way to Bergama, it is more convenient. To get to Otogars your hotel can easily arrange you a taxi, to Ayvacık is 17kms and to Küçükkuyu is 30kms. Both destinations are about 40-50 Turkish Liras. During winters, catching a taxi makes more sense whereas in summers from the front of the local coffee place 'kahve' right in the heart of Behramkale or down from the old port there are frequent minibuses parting for both Ayvacık and Küçükkuyu.
Once you get to any of the two Otogars ask for Bergama, they will either arrange you a bus company that goes directly to Bergama or another minibus ride to a busier intercity bus terminal in Edremit from where you will get a bus that drives you to your destination. From the bus terminal of Bergama you may still need a short taxi or a minibus ride to the sight. From there you can walk or enjoy a cable car ride. Departing from Assos to get to Bergama/Pergamon you need at least two transits. As I always suggest: Rent a car, it's safe, time saving and you can enjoy off the beaten track. The remains are alluring, the steepness of the theater is captivating. The photos are from my recent visit, I recommend early hours or afternoon hours for the visit.