- There is only one script file that loads and executes on the Arduino
Correct. There is no operating system so it just runs one program. Although there are ways of making it "look like" it's multitasking, or you can have a menu to choose between different operations/functions so it "looks like" you're choosing between different programs, etc.
- The best method of communication between the two is through USB serial
I'd say that's the "easiest" way.
...I've never used a Raspberry Pi.