I'm only going by the 2013 editor, but I think it's possible.
For Level 4 you would need to create three competitions:
"Second Division East/North"
"Second Division West/South"
You will need to register the teams to these two leagues.
The third competition will be "Second Division", and will have no teams registered for it.
When you're adding the leagues to the structure do not add the North/East and South/West. Instead you need to add "Second Division", but tick the box saying that it contains Sub-divisions and when prompted choose the East/North and South/West leagues as the sub-divisions. This sets both leagues on the same level, and you can choose which league the teams are promoted / relegated to.
I can imagine Levels 5 and 6 are the same; you will need to create five league competitions, one for each section (with teams registered to them) and one league which is empty.
It might help to look at the Blue Square North/South and see how that feeds into the Blue Square Premier League.