I am having a bit of trouble understanding how applications and data are accessed by the CPU from RAM after the application has been loaded into RAM and a file opened (thus data
You seem to be asking about addressing modes. At the risk of gross oversimplification (ignoring caching, segments, and logical memory), memory stored as a sequential array accessed by an integer address.
The CPU has a number of internal storage areas called registers. We will call them R0 to Rn. The processor assigns some registers dedicated purposes. One of those registers is the PC.
One common addressing mode is deferred. I indicate this mode as (Rn). An instruction like this:
MOV (R0), R1
uses the value contained in R0 as a memory address, fetches the value stored that memory location, and stores a copy of that value in R1.
An instruction sequence like this:
MOV (R0), R1 MOV (R2), R3
is stored in memory as data (ignoring protection), code, data, and variables all use the same type of memory. In other words, any memory location can be interpreted as code, data, or variable.
The CPU executes the next instruction located at (PC). After executing the instruction, the CPU automatically increments the PC to point to the next instruction.