How does the amount of energy avaiable at each trophic level affect the structure of the ecosystem?

You are correct about the 10%- there is only about 10% of the energy gained going from one trophic level to the next (the other 90% is lost).
  This is THE reason why there can't be unlimited levels in an ecosystem- it is MUCH TOO INEFFICIENT.  
  In a very short time, you reach a level (3 or 4 levels up) where you can't go higher, because there just isn't enough energy available.  They would need to eat so much of the lower level that that level wouldn't exist and the whole ecosystem would pretty much collapse.  So, that level won't happen at all.