Thank you for using Braph. I hope that it will be a useful tool during your research.
You cannot load the correlation matrices in the current version of the software. However, with a minor modification of the software you can adapt it so that it can accepted matrices calculated from external sources.
We discussed this problem previously on this forum, and I provided a series of steps that will accomplish your purpose. You can find the detailed explanation at: http://braph.org/forums/topic/eeg-graph-analysis/.
I hope that this works. If there is anything additional I can do for you, please do not hesitate to ask.