About low-level graphics programming, this will give you a lot of information: http://www.osdever.net/FreeVGA/home.htm. (It's very interesting for text mode as well.)
What will I undoubtedly run into that will confuse me?
You will realize that on PC there's an awful lot of stuff that is unclear: the x86 instruction set itself is complicated, and when you get direct access to hardware, it can take quite a while before you understand how to write a single character on screen.
Don't worry about floppy disk and such, most of the time you will use an emulator such as Bochs or QEmu.
