Hi, I'm very much a newbie when it comes to this. I know how to solder, strip wires, and shrink wrap them but I don't know the technical stuff when it comes to electronics.
That being said, I'm trying to wire this project as pictured. I know I'm going to be using a bread board for testing and development but when I'm finished with that and want to supply my circuit with a battery, how do I connect all the wires that overlap?
For example all of the groundings need to be connected to the MCU gnd and there's 4 components. Do I solder all the wires together, connect it to a single wire, shrink wrap it, and then put it into the MCU? Do I have to buy a wire connector?
The correct answer to your question is that if your project is to become a permanent installation then you do not use Dupont connectors for any connections. Rather you solder everything securely in place, preferably on a PCB or perhaps on perforated board. This is helped enormously by using the correct Arduino such as a Nano instead of a Uno, for example
You're kind of in a Catch 22 situation. As @UKHeliBob stated, the dupont type connectors are not very reliable but they are easy to prototype.
Regardless whether you know where all the pins go you would be foolish to solder it all together without testing for function first. If you put header pins on your MCU, you could test the functions before soldering it all together.
Then you could:
Solder the MCU pins to a copper clad prototype board
Use a good quality female header for the MCU and solder the rest. Again with a copper clad prototype board.
I've had good luck mounting the MCU board using quality strip headers. Something like these..
3D printed. This one uses 12 Ga solid wire. The .STL file is on my Talking Alarm Clock project page. It's fugly, but works well. Soldered connections are really required for power leads. Then you toss a screw shield on the CPU for the signal lines and you're done.