We are happy to help with any questions you may have about GenomeBrowse.
The Human mitochondrial reference sequence is included in the reference sequence for the entire genome build. Therefore to be able to load mitochondrial data you will need to either have Reference Sequence, UCSC or Reference Sequence, 1000Genomes downloaded locally on your machine you will then want to select the corresponding build from the drop down menu (GRCh37hg19 or GRCh37g1k respectively).
The difference between these two sets is the length of the mitochondrial "chromosome" so you will want to make sure and pick the correct one for your data, for the UCSC build it lists ChrM as being 16571bp in length and for the 1000Genomes build it lists ChrMT as being 16569bp in length.
We are in the process of adding in the functionality to load your own reference sequence from a supported data source (ex. TXT, FASTA, etc.) and will let you know when it becomes available.
Let me know if you have any further questions.