Hi
I just want to add to the thread here, as I am facing the same problems. 

I have an Atmel-ICE Jtag download/Debug box (In fact a white Atmel SAM AVR JTag box) connected to an AtMega2560 board and my PC. This setup is working perfect, when I am working in "pure" Atmel Studio mode. As shown in the  figure here, where I have downloaded code to my AtMega2560 board

When using Visual Micro in either Atmel Studio (7) or Visual Studio (2019), I can't upload my sketch to my AtMega2560 target using F5 (start Debugging and Break). Hence loosing the JTag debugging facilities. In Both Visual Micro for Atmel Studio and Visual Studio, I have tried all possibilities for selecting the correct Hardware Programmer. But with a negative result for all of them.

The reason for me/us that we want to have JTag debugging capabilies up running in Visual Micro, is that we have to show these in an educational purpose. We are planning to buy a bunch of NodeMCU micros and a bunch of the white Atmel SAM AVR JTag box as well. As the NodeMCU device isn't supported in Atmel Studio, we had to find another development environment to put focus on. Hence we are now investigating Visual Micro. If the chances having our current choice of Micro and JTag box working in JTag debug mode is to low, we have planned to look at the ESP 32 device with another JTag box.

I know the last part of my post is a bit unaligned with the first part of my post. But if anyone with a good ESP<xx> knowledge should happen to read this post, I will be very happy to get some feedback on the last part here as well. We don't know too much about the different ESP<xx> processors, so feedback here will be much appreciated. 

Actually I was not using default Atmel Studio (at least I think  . But to exclude this point from the issue here, I have been working entirely in Visual Studio now. 

Here I face the same problem though. I can't upload my sketch to my AtMega2560 board using the Atmel-ICE JTag debugger. 

Another problem is that I can't specify my Atmel-ICE as my HW Debugger. From various videos on the nex including this one : https://www.youtube.com/watch?v=SGxPpU8umqc, it should be possible to choose a HW debugger from a predefined list. But the only options I have in my project(s) is these 2 :
1) Manual/Custom
2) GDB
So how can I set up the predefined list of HW Debuggeres here ???

I have zipped my project and placed it here : https://drive.google.com/file/d/1Y9fg5eZaKiLBPLM_6CaNG8D7ulzvFP94/view?usp=shari... .

Hopefully it will clarify things, if you could have a closer look at it.

I have set the programmer to Atmel ICE. I just don't have any possibilities for choosing this debugger as my Hardware Debugger. I "only" have the 2 options seen in the attached figure below. This figure also shows, that I have enabled the ATmel-ICE as "uploader" in my project.
And as mentioned in my last post i can't upload using the Atmel-ICE. I receive an upload error. 
When using the Atmel-ICE as "uploader" and debugger in a "pure" Atmel Studio project everything works as expected. So the Atmel-ICE should be both connected and functioned as expected. 

Thanks, in device manager what is the usb driver name and version that shows when you connect the ICE?

Thanks for all the info. To upload Visual Micro passes the work to avrdude.exe. You can see the cmmand line to perform the upload in the output you have posted. The final error is "avrdude: usbhid_open(): No response from device"

d:\Programmer\Arduino\hardware\tools\avr\bin\avrdude "-Cd:\Programmer\Arduino\hardware\tools\avr/etc/avrdude.conf" -v -patmega2560 -catmelice_isp -Pusb mega2560\Debug/AtMega2560_Projekt1.ino.hex:i" 

avrdude: Version 6.3-20190619
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2014 Joerg Wunsch
         System wide configuration file is "d:\Programmer\Arduino\hardware\tools\avr/etc/avrdude.conf"
         Using Port                    : usb
         Using Programmer              : atmelice_isp
avrdude: usbhid_open(): No response from device


Therefore you can look for a solution for avrdude and ICE failing. I found a similar post here where the user explains how they resolved https://www.avrfreaks.net/forum/atmel-ice-avrdude-cannot-find-device

I note the user refers to libusb. It is also possible that an easy solution is to replace the ICE usb driver with one generated using tyhe libusb utility. Atmel do often have a clash between the usb driver that atmel studio installs and the usb driver that atmel avrdude.exe expects. This is a useful utility that might take care of it all for you https://zadig.akeo.ie/


Hopefully you can find the solution.

Our list of supported debuggers can be seen on the below page, and supports ESP32, SAM, SAMD, along with some support for MBED and STM32 boards.
https://www.visualmicro.com/page/DebuggerSupportList.aspx

And there are also more specific articles showing the in-IDE options for each set of boards, in the "Gdb Debugging" section of the Document Index: https://www.visualmicro.com/page/User-Guide.aspx?doc=index