Based the the specs I found for the TG16, it has 8 KB of RAM. I also found notes in the documentation of many opcodes that there is data stored in several "flags and switches" are these stored in RAM or in a designated register?
You are probably referring to the status register. This is a hardware register in the CPU, and is not stored in RAM.
Generally speaking, the HuC6280 is similar to a 6502-family CPU. You may want to acquaint yourself better with those parts; familiarity with them will make the HuC6280 easier to understand.