In addition to the Flash and RAM on the micro-controller, there is a chunk of address space dedicated to the peripheral registers. These registers provide the interface to all the peripherals which are probably the reason that you chose the mirco-controller. There are two ways that the peripheral registers can be addressed. The first is via memory access. Usually there is a dedicated hole in the memory space which addresses these registers instead of RAM. That means that load and store instructions to these addresses will handle reading and writing to the peripheral registers.

The second approach is via special instructions. The AVR uses this approach to access the lowest registers. The intention is for these to be the most commonly used ones, but it never seems to work out that way. The limited number of registers that can be accessed this way is because there are only a few bits available in the opcode to act as addressing for the instruction. In order to access all the other registers, they must be addressed by the first approach. On the AVR this method only take one instruction while the first can take 3. Two instructions to setup an address pointer and one for the load or store immediate. Thankfully, the gcc compiler will handle figuring this one out for you.

The small PICs have their own oddities as well. Instead of using 16 bit addresses to access RAM, they rely on a concept of memory banks. In order to access memory, a bank has to be set which determines what memory can be addressed using the load and store instructions. For each bank, there is a chunk of addresses devoted to registers, followed by RAM, and a small chunk of common RAM. The common RAM is the only part that is the same no matter which bank is selected. Accessing memory that is all in the same bank is compact, but if several items need to be transfered between pages then a lot of instructions are wasted shuttling the values between banks.

Typically Flash is read only by the instruction fetcher based off of the program counter. However when writing to Flash you often need to consider that it is composed of what are known as blocks and pages. A block is a chunk of Flash memory which has to be erased as one unit. A page is a piece of Flash which has to be written as one unit. Typically a block contains more than one page. If you never plan on writing self modifying code (bootloaders) then you will probably never need to worry about this. But if you need to change portions of the Flash you will need to handle erasing at the block level and writing at the page level. If you wish to modify only parts of the Flash, then you will have to store the previous values, erase the block, and rewrite all the pages.