If i can put the wires in the boxed off section, can i use normal
wires or do have to be in some sort of trunking?

Trunking, conduit, or some sort of divider to meet wiring regs unless the
separation is large enough, also you need to think about the temperature.
Unless space is very tight you shouldn't have to chase the wall though.

Invest in one or the Whitfield or Scaddan books, or the IEE "On Site Guide".