I think you're asking two different questions there.
The first is more about how to deal with disaffected learners. Just because a child's behaviour is bad, it doesn't mean they don't have the ability to complete the work you're asking them to.
The second is more about students who genuinely don't understand something after you've explained it the first (or second, or third, or fifth...) time.
In both cases I think the key is to deploy a variety of teaching methods so that students are not always doing the same type of activity all the time. This increases the possibility of a high percentage of the class being engaged by the topic and understanding it.
However, this won't work all the time. You do need to have the patience, with lower-ability students, to explain the task or concept more than once. If you're intelligent yourself (which I'm sure you are!) then with luck you should be able to work out different ways to explain the same idea (clearly if your first explanation didn't work, then you need to try another way). You also need to make time in your lessons for regular progress checks - not just asking the whole class if they have any questions (as some students won't want to reveal the fact that they don't get it in front of all their friends) but also going round the room and seeing students individually, encouraging high-ability students to help those around them once they've finished their own work, etc. Lots of strategies you can use.
With whose who are badly behaved, as well as sticking with a variety of teaching methods (within reason....you're not a performing seal!), you also need to stick to the school's behaviour management policy. Make clear to the kids from day one that you do know it inside out and that it will be applied (stress the inevitability of it, not the severity). Escalate sanctions as per the school policy. It may well be that eventually you have to use detentions, that children may have to be removed from your classroom etc. It's sad but there will occasionally be kids who persist in misbehaving (not just for you, but many of their teachers), and if they ultimately stop others from learning then it may well be that you're unable to keep them in the room and give them the chance to learn.
Hope this helps a bit.