The ivtec doesnt have speaker space in the rear doors, it only has speakers in the front doors and the rear boot shelf.
yes, change the front speakers to aftermarket speakers, buy Pioneer 1720 or Fusion EN-CM65 (9k)
JL Sub in the boot (6k with enclosure)
a 4 channel amplifier ( second hand would do, but buy a branded amp, not chinese) 7k
and 2k for fitting and wiring, this would increase your total budget a little bit, but would pay off..and components are usually 6.5inch in size, civic comes with a 5.25 or 5.75 inch speakers..but size is not an issue, spacers are used to fit the speakers.