Hello Jerry,
1) "are there any plans to improve the background geolocation support for Appery" in Appery.io the geolocation phonegap plugin is used. So as far as I know there are no plans for its modernization.
2) In principle, you shouldn't make nae changes in Eclipse. Everything that can be done in Eclipse you can do in Appery.io builder.
As for adding plug-in IOS - there are any changes here, only via xCode. You can develop an application, and when the time comes to test on the device - export in xCode and add the plug-in there. Test and after that, continue to develop the application in Appery.io builder