Your problem has two parts, parsing the time and getting the difference:
NSDateFormatter* dateFormatter = [[[NSDateFormatter alloc] init] autorelease];
[dateFormatter setLocale:[[[NSLocale alloc] initWithLocaleIdentifier:@"en_US_POSIX"] autorelease]];
[dateFormatter setDateFormat:@"mm:ss:SS"];
NSDate* firstDate = [dateFormatter dateFromString:@"01:00:00"];
NSDate* secondDate = [dateFormatter dateFromString:@"01:02:00"];
NSTimeInterval timeDifference = [secondDate timeIntervalSinceDate:firstDate];