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Different parts of computer systems, including communications, to work optimally, often need to coordinate their time, or work using coordinated time and so "clocking" is the process of keeping those different parts' times coordinated.
In our world, if you wanted to take multiple buses/trains/flights to get from one place to another, you'll probably want to know their scheduled departure and arrival times. Knowing that, you can plan your trip using the least amount of time. For this to work well, though, you and all the buses/trains/flights need to agree to use same time from the same "clock" (in our world, it's based on UCT). However, beyond agreeing to use the same "clock" time there's the issue of keeping everyone synchronized to it.
In the computer world, communications senders and receivers also need to coordinate using the same "clock" time. Keeping synchronized to the same "clock" is "clocking".
As your OP noted "clocking" might be embedded in the data signal or it might be a separate signal. If a separate signal, it's often on its own wire, and as wires often terminate in plugs, and those plugs have pins (or sockets), particular pins (and sockets) are dedicated to specific wires. So, a certain plug's pin (and socket) might be assigned to a separate clock signal.
