The raw marks are what the markers award for your responses.
The aligned marks are determined by a team of judges (standard setters) who use the exam paper, the marking guidelines and the Performance Descripter Bands (the things that say what a student at each Band level should be able to do). They decide what the cutoff on each question should be for a student at the cut off point e.g. in a 10 mark question they might feel that a Band 6 student at the 89/90 cut off should be getting 9/10 but for the next 10 mark question feel that it should be 7/10 because it was a harder question. After they have done that with the entire paper the cut offs are totalled and a cutoff is determined which could be something like 83/100 = 90/100.
This is done on a subject by subject basis and is aimed at meaning that a Band 6 in 2008 was equal to a Band 6 in 2002.
Once this process is finalised the BOS hands all the marks to UAC who then scale the marks based on the results of all students in all subjects to match them up.