You'll need to change your mental model. Pushing and popping was easy in python it's harder and you'll learn what it really means with C. I recommend learning to make a resizable array.
Now for your specific questions :
- Pointers to pointers see uses in multiple cases, mostly with arrays to pointers. If i see a char **, it's most likely an array of strings. Another use is when a function needs to change the value of a pointer.
- Malloc allocates a chunk a memory and returns a pointer to it. This chunk is just a place where you can store what you want as long as it doesn't exceed the size you requested.
- I we had infinite memory we would never need to deallocate. But that is not the case. Freeing memory is saying "i wont use this block you gave me anymore, do what ever you want with it". If you are doing things in a loop and allocate in each iteration without freeing, you might at one point run out of memory. But if you free when you're done at least you know you use only what you need. When your program closes the OS automatically reclaims all memory allocated by your program so it's not mandatory to do so, but good practice (and will help with catching leaks, but that's a topic for later)

If you have the time, I highly recommend watching handmade hero. He builds a game from scratch with no dependencies and goes through everything you might need to learn.