[Solved]-Highcharts plot MACD + EMA + Volume-Highcharts

The macd indicator is displayed in the second pane, but comparing to the volume series, the values are very small and macd is just a flat green line.

You need to assign the macd indicator to a different y-axis.

series: [..., {
  type: 'macd',
  yAxis: 2,
  linkedTo: 'aapl'
}, ...]

Live demo: https://jsfiddle.net/BlackLabel/Loqrua4w/

As to your second question:

Also, in case of adding multiple panels, is there a way to auto fit all the panels instead of specifying height in percentage?

There is no such logic in Highcharts, but you can easily calculate percentage values by your own script.