it can affect you very negatively, for history extension i got 47/50 for hsc, but my internal ranking was 3/5 and the 3rd person got 39/50 so i got brought down to 43. try to go up by ranks, or make sure you and everyone in your class does well.
it should be fine, my school's dux was working while doing her hsc and she got a 99.6 atar, she did 3u eng, science ext, standard math, chem, bio, economics