I would recommend the following resources. Quantum annealing is about QUBO/Ising formulations. First thing would be to get familiar with the formulations, and see examples of how do you formulate a few problems:
A Tutorial on Formulating and Using QUBO Models
Ising formulations of many NP problems
Then, if you have a specific problem you would like to ...
There is no guarantee the lowest energy solution get picked more often, or even get picked once.
Many parameters may be tweaked in order to improve your results. I am not sure if you are running time parameters by default but you may tweak more the times (like longer annealing time...).
Secondly, it may be the case that this problem corresponds to a hard ...