Have been returning on and again evary year to Bali for the past 6 years, (you can chekc my gallery here https://www.flickr.c...157627401970335
there are three areas I would recommend : Tulamben, Lembongan and Padang Bai.
First off I suggest you move from place to place, rather than staying at one place and having long car rides every day, taht said you can dive Lembongan/Nusa Penida from Padang Bai.
Tulamben is better when dived from Tulamben, some would advise staying in Amed, I don't because Amed dive centres and guides are clearly one or two steps below Tulamben's. Tulamben is mainly black sand macro and the Liberty wreck,
For staying I prefer Tauch Terminal, however I don't like diving with TT, I book my dives at Liberty dive centre they provide you with free nitrox and private guide included in your dive price. They pick me up each morning with their truck, I just schedule my preference with my private guide.
You can also stay at Liberty dive resort where the dive center is located.
Padang Bai, I'm using Gekodive for years, they have good guides as well for local dives. The jetty is not t be missed if you're on for rhinopias and lots of frogfish under a pier. they also rovide diving to Nusa Penida, without having to stay on Lembongan.
Best option for staying nearby : Puri Rai hotel.
Lembingan has evolved much to a cramped backpackers place these past years. I don't stay anymore on Lembongan.
Twofish used to be good, the bungalows are fine too but the recent management is not up to the past one, they have speedboats which is a good point. Worlddiving is also an option but their boats are often crowded and one is too big for serious diving.