The answer is that it doesn't use LevelDB for this.
It has an in-memory data structure with all known block headers, each pointing back to its parent. It also has a vector with pointers to all block headers in the currently active chain.
To build locator objects, it simply looks in this vector at specific indexes.
I want to be able to control how the different nodes are
interconnected to each other in this network. Is there a way to do
this on Bitcoind?
As per bitcoin.conf I suggest setting up the connect = X.X.X.X flag on your nodes. It will enforce connecting only to the peers specified by you. Not sure if this is the answer you are looking for though?