You have a few options.
Option 1: Classical
You go to check in and they check you inn as they usually check in the families. If you ask and tell them your wishes, they are usually kind enough to satisfy your wishes.
Option 2: On-line check-in the day before
If you do the on-line checking one day before, you can choose your own seats as you like. If your children are more than 2 years old, they always get their own seat. Safety policy is, that every child must seat near adult, so in case of emergency, the child has help.
!!!! If you fly with low cost airline, that is not always the case – you may end up boarding as last and there are only 2 seats left separately. If you talk to passengers, usually they are kind enough to change seats so you can seat with your child, but it is not the case every time. So make sure if possible, that you board as soon as possible, preferably the first!!!
We usually choose to sit in a 2 rows, together one adult and one child, so one could amuse and entertain one child. That suited us the most, but it is really up to you what suits you most.