Don't worry about the confusion. It's confusing the first time you start reading about it.
This is a stripped down explanation (and I still apologize for the length). I know I skipped on some details and glossed over some points, but here is the general idea:
In the beginning, 1 cpu was 1 piece of silicon with 1 physical core on it.
This 1 cpu could only do 1 thing at a time, but it was very fast. If you told it do do A, it did A very quickly (the act of doing A ran within 1 thread). If you told it to do A and B, it could do a little bit of work for A then switch and do a little bit of B. It did this so fast that the user thought it was doing A and B at the same time. It could continue switching back and forth between A and B until both were finished.
In this simple scenario, you have 1 CPU with 1 physical core that was running 2 threads.
Developers realized that there were some parts of their application that could run "at the same time" in multiple threads. A good example is your web browser. You can enter a URL, hit enter, but the browser is still "listening" to the mouse so you can hit the stop button. That's (at least) 2 threads: 1 thread to go to the URL and get the web page and 1 thread to listen for the mouse.
So you still have A and B running, but A could have dozens or hundreds of threads and so could B. The faster the CPU, the faster it can switch between all the threads in A and B.
This worked fine as long as the CPU clock speed (measured in GHz or MHz) kept getting faster, but eventually they couldn't make them faster. Manufacturers simply couldn't make them run faster without making them so hot that they melted (or you used liquid nitrogen to keep them cold).
Enter hyper-threading: the CPU isn't just 1 little part. It's actually millions of parts working together. Some parts are used all the time and some parts designed for specific tasks (they could perform other tasks as well, but were REALLY good at their specific purpose). If you weren't doing anything that needed that specific task, then it just sat there doing nothing. Then they had a brilliant idea: what if you took those special parts and used them all the time to run a 2nd thread. It wouldn't be as efficient, but it would work. They called this hyper-threading.
Now you could have 1 CPU with 1 physical core and 1 logical core (the term for the extra stuff that was now being put to use to pretend it is another CPU). At this point, you could actually work on 2 threads at the same time.
Then they had another idea: what if instead of 1 CPU (that was hyper threaded) on 1 piece of silicon, you put 2 physical CPUs on 1 piece of silicon. Now you could process 4 threads at a time.
This trend has continued. Your Mac Pro has 1 CPU with 4 Physical Cores that are Hyperthreaded and capable of running 8 threads at a time (1 X 4 X 2 = 8).
The New Mac Pro (based on limited information) looks like it will have 1 cpu with 12 Physical CPU cores that are hypthreaded and capable of running 24 threads at a time.
I hope this didn't confuse you any more. Feel free to ask questions and I'd be happy to explain anything that's confusing.
Good Luck!!!