I will try to explain to you in short way. Yes it's true that they learn on their own native language, but it must be mentioned that only Albanian, Roma and Turk minority are part of this. Part of other minorities, like Serbian and Vlachs, are going to ethnic Macedonian schools, because they have almost same culture, majority of them use Macedonian as native language and etc.

They learn Macedonian language from IV th grade in the elementary school till the end of the high school education. 

Last year, the government tried to include the Macedonian language as a subject from the first grade, but the Albanian minority have protested because they thought it wont be good for their children to study Macedonian language from early ages. So till know, minorities learn Macedonian as separate language from IV th grade.

Situation is same at the high school system.

Although, at the universities where main language is Macedonian, there are hundreds of students from every minority who don't have problem to study on Macedonian. There are guaranteed places at every university for students who are part of ethnic minorities.

About separated schools, we don't have it in majority ethnic suburbs. But in the cities where there isn't any big majority, there's one school and for example Macedonian goes in the morning at school and the students from other ethnic group go after them.

I hope you will now get a clear picture of Macedonian education.