You get points for winning, drawing, or losing, and then extra/bonus points for qualification to the later rounds.
For example, two teams might have qualified for the semis, but one team might have 18.875 coefficient points, whereas the other might have 22.125. There is a way they calculate it. Therefore, all teams get equal points (bonus points) for qualifying to the same round. Hence, if both Juventus and Milan make the quarters, we both get 2.5 bonus points (if that is the amount allotted for qualification to that round); however, if Milan qualified by winning and losing over both legs, while we won both games, we get more overall points due to the nature of our qualification.
In the end the total number of points accumulated is a combination total points, bonus points, and wins divided by the number of games played and the country's coefficient and strength of the league, or something along those lines.