[ATMEGA128]IDE: Atmel Studio 7.0
Software Envirement
OS: Windows 10 Pro 64Bit (1607 Build 14393.447)
IDE: Atmel Studio 7.0 (build 1188, Official Direct Download Link, additional Infomation)
Tool Chain Contained 'AVR 8-bit GCC Toolchain 3.5.4'
Hardware
Target Board: NEWTC AM-M128-B(16Mhz Clock)
ISP: NEWTC AD-USBISP V3.6
New Project

New Project
'C/C++' Tab, 'GCC C++ Excutable Project'
Board Selection, ATMEGA128
Connect Device

Tools -> Add target -> JTAG/ISP -> Com Port
(If you unsure which com port, hit 'Device Manager')
Build Test
#define F_CPU 16000000
#include <avr/io.h>
#include <util/delay.h>
int main()
{
DDRG |= 0x03; //Connect onboard LED
PORTG = 0x00;
while (1)
{
PORTG = 0x01;
_delay_ms(500);
PORTG = 0x02;
_delay_ms(500);
}
}
//This Test Code means be Blinking every 500ms
Build Tab -> Build solution[Shoutcut 'F7']
Upload to Target

Tools Tab -> Device Programming -> Tool: STK500, Device: ATmega128, Interface: ISP -> Apply

Memories Tab -> Flash -> Program
Recommending way
Project pre-setting

'Project' Tab -> 'Hello_AVR' properties -> Tool -> Selected debugger/programmer -> STK 500, Interface ISP
go to 'Debuge' Tab -> Start without Debugging[Or Shortcut 'Crtl + Alt + F5']