The main difference between JCTA and JCTB is related to the the types of the papers that they publish. In JCTA the editors consider those papers with emphasis on combinatorics and don't accept the papers just about Graph Theory. But about JCTB the main emphasis is on Graph Theory. 
But about the best Graph Theory/Combinatorics journals there is no a unanimous agreement. One can consider journals like:
1. Journal of Combinatorial Theory Series A and B/ 2. Journal of Graph Theory/ 3. Electronic Journal of Combinatorics/ 4. Journal of Combinatorial Optimization/ 5. Graphs and Combinatorics/ 6. Combinatorica/ 7. Annals of Combinatorics/ 8. Discrete Applied Math/ 9. Discrete Math/ 10. Discussiones Mathematicae Graph Theory/ 11. Australasian Journal of Combinatorics. Although, there could be some other high quality journals.