I have an alienware m17 r4 with intel i7-6820HK @ 2.7GHz along with a gtx 1080.  I recently bought an alienware graphics amplifier along with the EVGA Gtx1080 ti SC2.  the system detects the card and all drivers are updated, but when I play games its still using the gtx 1080 as a card and not the gtx 1080ti in the GA.  I'm not sure what's going on here.  On the AW command center it shows that all gpu are ON also.  Please help me out on what I am doing wrong. 

Sounds like you need to go into nvidia control panel 3d settings and choose the preferred graphics processor/high performance gpu for each game/program you want to use. Otherwise I'm not sure if you can disable the 1080 in hardware settings but that would also be an option. I'm sure the addon box you bought also has an instruction manual if what I suggest doesn't help take a look there.

been trying it for an hour still have all gpu on when i get on step 8
 

Make sure you update your computer bios, download and install the graphics amplifier driver from alienware website. boot in safe mode, use ddu to uninstall all nividia drivers. Shut down computer, plug in graphics amplifier, boot computer, install drivers for 1080ti. Reboot.
 
Like suggested before, make sure you open nividia control panel and set 3d options to prefer high performance graphic card.
Also like stated before, you could disable the onboard 1080 before trying these steps.
 
I have done the same with my alienware laptop 2016 17 R3 and a evga 1080ti sc2 gaming hybrid.
It was really just plug and play for me. I had no issues. I just followed what i put in the start of my response.
 
I will check on things when i get home to see if i missed anything, but it was really simple for me.
I even cut out a window and put in some plexiglass so i could view the glory...
 
https://www.modsrigs.com/detail.aspx?BuildID=38957