Hi [NAME] welcome to this free user-to-user Alienware laptop discussion forum.  The Alienware 15 R3's system board (aka motherboard) has the onboard power supply circuit and this regulates distribution of power to all parts. The discrete GPU NVIDIA GeForce GTX 1060 will be correctly powered.  The OEM replacement Alienware 17 R4 / Alienware 15 R3 Original 6-cell Laptop Battery 99Wh is DP/N 9NJM1. 
My current battery doesn't hold any charge. It's the 68Wh 15.2V with GTX 1060 and I want to replace it with the 99Wh 11.4V. Some say it's fine to replace the battery with different volts and the laptop will adapt to it. But the 99Wh battery is used for the GTX 1070 and 1080. Will using this battery damage the GPU? Or will it not be able to function properly since it's GTX 1060? Sorry if my English is poor.
15 R3, upgrading battery from 68Wh to 99Wh