In the engineering course, there were only 3 more male students than female students. Or In the engineering class, the male students outnumbered the female students by three. Hope this helps

6 male and 3 female

In the Engineering course there were six male students and only three females. There were only three female students compared with six males in the Engineering course. The engineering course had three female students and six males. Six male students were studying Engineering compared with three females. Males outnumbered females by a factor of two, in the engineering class. There were twice the number of males to females in the Engineering class. there are many ways to phrase this.

Do you mean there were 6 male and 3 female students studying engineering, only 9 of them? Or the proportion of male to female students was 6:3? Or the number of male students was more then the number of female students by 3-6 persons? Say, 26 male and 23 female