Great that you got the whole thing set up, that's the first step!
If you never programmed in C, I really recommend you to read books / websites / video tutorial about how to code on the language as the next step :).
To answer your question, you can (and will) write code anywhere is the file (more or less). The gameplay code will most likely go after the "put code here" comment. But when you want to use a variable, you'll have to declare it first, so you'll most likely declare the variables after the "#include <snes.h>" file.
If you trip on color restrictions or audio restrictions, you'll usually see it when running the game on emulator: nothing will show, or the color will be wrong, etc. (retro game development is usually quite scare when it comes to debugging tools :p)
Regarding input, PVSNESlib is quite nice as it accepts:
- BMP for graphics (be careful of the color palette, it needs to have 256 color palette BMP with only the first 16 or 4 colors defined depending on the graphics mode you'll use - usually it'll be 16).
- IT (Impulse tracker) for music and sound effects, if you use the "non-streaming" function. I recommend OpenMPT as a program to create those music and audio files (it's arguably the best "modern" tracker program available) https://openmpt.org/
- WAV for sound effects if you use the streaming functions (beware, it does work well only on NTSC, and it's quite complex to use - I recommend sticking to IT file for beginning)
You can open the source code of Keep SNES alive to see an example of that, the archive contains everything: code, images, sound, music, etc.
But as I said, you should really start by learning how to code in C first, else you'll have an hard time doing anything meaningful. You don't need to take a full course, but at least to learn the "basics" (using and typing variables, loops, creating functions, etc.)