ariefpn,
Have you installed the latest version of PhoneGap in your machine? For instructions to install latest PG version, please check this link: http://docs.phonegap.com/getting-started/1-install-phonegap/cli/
Once you have installed the PhoneGap 6.x successfully, open MyEclipse and add a new PhoneGap runtime pointing to the PhoneGap folder (<npm install dir>/node_modules/phonegap) in your machine (Window > Preferences > MyEclipse > Mobile Tools > PhoneGap Runtimes and click Add). Select the newly added runtime instead of the Embedded MyEclipse PhoneGap.
In the New PhoneGap Application Project wizard, the Target runtime by default selects the runtime you selected in the Preferences page. If you are doing a local build, then you should also update the Android tools to support PG 6.x builds.
Hope this helps. Let us know if you see any issues.
–Swapna
MyEclipse Support