Hooberus,
Chimpanzees don't factor into this at all. The time-point for human chimpanzee divergence is a separate matter....that uses a different method....a popular one is the difference in cytochrome c sequences and its changes are dependant on nuclear DNA mutation rates - not mitochondrial DNA.
LIke SNG wrote you only need to know how much change has happened to the sequence over time and how much time it takes for that change to happen (i.e. rates for human mitochondrial DNA - In the late eighties when the first paper came out, the rate was pegged at about ten times higher than that of nuclear DNA, but since then its been found to be higher...so thats why the age for mtEve was reduced somewhat if you're wondering).
They only had to look at the mitochondrial DNA of the individual people they sampled and find the amount of changes/differences among the sample.
They then fit the samples into a geneological tree (one which fits in all the samples but that requires the least amount of changes overall - you see they're not trying to inflate the age)....that gives a relative outline of which sequences were ancestral or descended from which. The rate can then be used to figure the age.