Possibly the biggest shift for teachers using Khan Academy, say compared to tools like Mathletics or Mangahigh, is the stance Khan Academy takes; the student in control, the teacher is 'merely' a coach, or guide, which is pretty fundamental shift if you think about it. So use Khan Academy to give the students the freedom to explore Mathematics, to go where they will, encourage exploration and inquiry! That said a bit of guidance is good, so Khan Academy gives you the power to more subtly guide/coach the kids rather than control them.
The is best done by setting a general 'locus of focus', called a 'mission', that's their 'centre' or hub. They can venture out from there where they will, but that is the area they will return to, and where they will spend most of their time working. This 'venturing out' could be up (more complex) or down (more foundational, revision) whatever they feel they need. I regularly encourage Grade 5 students to work on Early Maths, if for no other reason that to know/remember what real Mathematical fluency, feels like.
Students should try to focus their work around the Mission for their grade, or the grade below (good for consolidation/practise), and bookmark that as their 'go to' space in Khan Academy; here's a bunch of links they can use for each grade level:
It should look something like this:
Focus on mission level practice, and mission completion. If you complete the Grade 5 mission, I'd advise you to go back and complete the missions for Early Years, Grade 3, and Grade 4 - it's all good practice, I did!
From time to time your teacher's recommendations will at the top of the list of 'skills up next for you', obviously do these first if you can.
This is really good if you're finding an activity hard (even homework) then you can track back up the 'tree' to an earlier skill that you probably need to practise or master before you try and do the activity you're finding hard to complete.
As a class coach (teacher) you have a few of tools available to enable you to effectively coach your class, from a micro focus on each specific student , which is the 'Student Progress' area. Probably the most useful though is the whole class 'macro' focus in the 'Skill Progress' area, which you can think of a bit like the contents page of a traditional Maths textbook, but a LOT more powerful.
From here you can see at a glance how the whole class is coping, and you can point (recommend) that all or some students work on specific Maths foci, eg subtracting decimals, or making 10 using grids, whatever you desire. It doesnt matter which the core mission is that the class is working on, you can select any maths skills from the Mission menu, or identify the kids who are struggling (ie learning) with one click.
I also really like the knowledge map, or 'exercise dashboard', here's a link that should take you there:
It should look like this: