I am happy to help you with your GenomeBrowse Questions.
The Revised Cambridge Reference Sequence (rCRS) of the Human Mitochondrial DNA is contained withing our full GRCh_37_g1k version of the human reference sequence. The track is labeled "Reference Sequence, 1000Genomes" and can be download or streamed through the Annotations Tab of the Add dialog.
To use this reference sequence to visualize your BAM files you will need to make sure the header for your BAM correctly identifies the name and length for the mitochondrial region of this track. For the 1000Genomes reference sequence it is chrMT with a length of 16569. You can see what information is contained in the BAM header by loading the file into GenomeBrowse then clicking on the plot name in the Plot Tree and scrolling down to the bottom of the Console.
If you receive any errors it would be easiest for us to diagnosis what is happening if we could take a look at your BAM file directly. If you would be willing to share your file please email us at firstname.lastname@example.org and we can arrange for a secure transfer of the information.
Please let me know if you have any further questions.