In the current version of Energia it is not possible to set a custom upload command. We are working on a new build system that will allow you to do this but we do not have a date for this. The only way would be to create a custom upload command in the IDE. The panStamp branch of Energia already uses the gdb-bootloader. You can find it here: https://github.com/energia/Energia/blob/panstamp/app/src/processing/app/debug/MSP430Uploader.java#L65