The best way to get around all the memorials, museums and cemeteries is by car. I had my own car hire which I hired in Istanbul and I came to the Gallipoli peninsula from Edirne near the Bulgarian border. I stopped off at Gelibolu (Gallipoli town), about 40km north of Eceabat, before spending the night in Eceabat and then exploring the peninsula the following day. It's a nice drive that was even more nicer as it was early January and I virtually had everything to myself. As it was, I gave two American guys a lift around the battlefields and cemeteries of the northern peninsula after meeting them in the Kabatepe Information Centre & Museum. I managed to see everything in both the north and south of the peninsula in a day as well as the Kilitbahir Fortress.
If you're arriving on the Gallipoli peninsula from Canakkale, then you have two ferry options: one that arrives in Eceabat and other that arrives at Kilitbahir where the old fortress is located.
The Canakkale-Eceabat ferry runs every hour on the hour from 7am-1am and then 3am & 5pm (with sailings every 30 minutes during the busy summer period). I took my hire car across and it cost TL23.
The Canakkale-Kilitbahir ferry runs at 7am, 8am, 8.30am, 9.15am (and at 15 mins past the hour until 6.15pm), then 6.45pm, and then every hour on the hour between 7pm & midnight. There are also extra sailings in the summer at 45 mins past every hour between 9.45am and 5.45pm.