How is the breadboard holes connected to one another

There are 6 parts of the board

4 side rails - usually use to connect positive and negative to power source (i.e. battery)
2 main parts - in middle use to connect electronic components (capacitors, resistors, transistors, etc)

Consider that each connection is like a cable / wires. Refer to how the hole are join / connected as in the diagram below.

1, 2, 3, 4 are the side rails (use to connect power source battery positive /negative)
5 and 6 - main part (use to connect component)

After you use it more and more gaining experience each day. The reason why it is build that way becoming clearer in your head. And then you can use the hole flexibly.

Example of use: 9 Volt Battery and LED

Connect negative to rail 1 and connect positive to rail 2. Then take an LED and put the pin between rows not the same row. Take a wire connect the LED negative to rail 1 and connect positive to rail two. The LED should lights up.

Keep practice one day you will how simple and why the breadboard connection is made in such a way.