Moderation is in relation to your own and cohort's marks. If one school sets hard assessments and another sets easy assessments, how you compare the two? Obviously 80% in one of them is not the same as 80% in the other, so BOS needs to moderate the school marks such that you can compare these marks objectively. This is done by looking at how you and your cohort has performed in the HSC - they perform calculations involving the mean of marks, the highest/lowest marks, looking at the range of marks etc. Your school marks can be raised, lowered, stay around the same, depending on your cohort's HSC exam performance.
Aligning is in relation to the HSC exam marks and performance. The exam mark/performance which is borderline between a Band 5 and Band 6 is set as 90, the exam mark/performance which is borderline between a Band 4 and 5 is set as 80 etc. Your marks are then aligned so you fit in these ranges and so you receive an exam mark based on a set standard. The same process is done to moderated assessment marks.
http://www.boardofstudies.nsw.edu.au/hsc-results/determining-achievement.html