Your CPU percentage might reflect that only one of your two cores is engaged in the work. In certain cases, MATLAB will automatically use multiple cores even if the user does not have the Parallel Computing Toolkit, but those cases are based upon doing mathematical operations on large vectors or arrays (usually around 9000 or more elements.)
I cannot determine at the moment whether your task would be suitable for parallel processing even if you had the Parallel Computing Toolkit, but it might be.
You should profile your code to determine where the bottlenecks are. You should ensure that you pre-allocate your matrices when computationally practical. These are unlikely not engage the second core automatically, but they have the potential for improving the efficiency of your single-core computation.