Using Splunk 6's embedded new maps you will NOT be able to change the pie charts for other labels and values. Check this related question and answer:
You could still utilise the google maps app within Splunk 6.0 to get what you need though.
Splunk has geolocation built into using the Google Maps app, link here:
However, I'm not exactly sure what you mean by replace a pie chart with map markers. Could you give a little more detail?
for example i have servers in certain areas and i want to know the util of all the servers ,so the area will be plot in the map and show the max cpu util in every area and change the color of the circle around it like in the google map.Is there a way in built-in map in splunk 6 to change the pie chart to map marker?