Newbie doubts

Hello everyone,

I am starting my way in networking. I have a bachelor CS background but never went deep in networking. Now I am working as IT support and willing to move forward in my career.

Studying for taking the A+ certificate, some doubts with TCP IP model came up in my head.

1. I never understood why is it explained backwards, like Application layer, where is everything starts, where the data comes out is placed last, and the physical layer, which is the layer where the data is transmitted between networks is placed first!
2. Also, with the physical layer, I don't get if it involves the local transmission with rj45 cables, router and switch or the transmission between networks, optical fiber and so on.

Clearly, don't getting this step is making me much harder to understand the processes involved in each layer. Do anybody knows good books or websites, bibliography related to this which could help me?

Thanks!