Work out what you most want to see and do. First night, Apollo Bay is more or less halfway sightseeing-wise, but if you want to do some walking in the rainforest, Lorne can be more convenient. Means a busier second day. If you want to visit Hopetoun Falls or the redwood forest, this works better staying in Apollo Bay.

Second night, if you want to see the 12 Apostles at sunset, then definitely stay in Port Campbell. You don't want to be driving around after dark because of the high chance of hitting a kangaroo on the roads. I prefer Warrnambool, however, greater choice of accommodation and eateries and the sound and light show at Flagstaff Hill is worth doing. Plus it's a lovely town.