For your second question, in Braph you could import a brain atlas in .txt, .xlsx or .xml file. Therefore, you could import the atlas coordinates from any software by first exporting them to one of the above formats and then importing that file into Braph. Please note that in order for Braph to be able to read the brain atlas file it needs to be prepared in a particular way, as explained in the above link.
I hope that this helps you. If you need any additional information please do not hesitate to contact me.
Currently in Braph we implemented only between group analysis in which the statistical significance is reported by non parametric permutation tests. The withing subject design is not implemented in the current version of Braph.