What is the overall theme of this book? It seems like there are multiple themes and meanings—it's kind of confusing.
You are right, it is confusing because Voices in Time does have multiple themes, but if I had to choose one central theme it would be breakdown of communication. Not only does communication breakdown cause the apocalypse, but it also foreshadows it.
For example, look at the breakdown of communication between father and son. Both Timothy and John are in full revolt against their fathers' authority in their lives. There is a breakdown of communication there and, as a result, the sons participate in some very unruly behavior: Timothy tries to expose one of his father's big-wig Pentagon friends and John rebels with unsafe sex and drug use. These two examples are perfect examples of foreshadowing the apocalypse.
Of course, what is the apocalypse? Is it a cataclysmic asteroid hit? Is it an unholy demon? No. It is a simple breakdown in communication. What destroys civilization in Voices in Time isn't any one person or any one thing at all. Instead, it is simply caused by the overwhelmed computer system as it becomes more and more global.
“It was as though the whole world was thrown back six or seven hundred years without having the organizations those ancient peoples had." He paused, breathing heavily. "Of course, there were many survivors who understood small skills. Some of them would repair small engines, but they couldn't manufacture them. They couldn't refine fuels. Fortunately a good many doctors who had practiced in small towns and in the country survived. They had their medical books, but they could no longer get the drugs they needed. Anyway, medicine survived after a fashion. Then gradually little patterns of order began to appear and another Bureaucracy came into being.”
The world had become dependent on that instant communication, in fact, that instant gratification. Now, without that communication, humans are forced to revert to the time of the ancients. No one currently living had any real skills. Further, if they did have skills, they weren't able to produce a product from those skills. It turns out that every single level of manufacturing has so much to do with communication that, with that one element taken away, the world virtually ends. It is interesting that John dies peacefully after the story of the Wellfleet family is finally read and digested. Why? Because that is the beginning of communication!