Hi Bogdan,
I am so sorry that we don't have WinCE BSP for i.MX6. so you cannot build the firmware using our MFGTool2. But our third party provide the WinCE BSP for i.MX6, this mean that you could connect the third party , if the third party BSP support MFGTool you can use it to build the firmware~~ Hope this can help you ~~
Best Regards
Dan