I have an Atmega328PBXplained board and I get errors when trying to upload to it.  I tried the basic Arduino Blink sketch and it compiles.  Here is the uploader output:

Uploading 'test_blink_debug' to 'Atmel atmega328pb Xplained mini' using 'COM11'
Uploader started for board Atmel atmega328pb Xplained mini
Upload method will be: bootloader
Uploading via Bootloader
.3.0-arduino9\bin\avrdude e\6.3.0-arduino9/etc/avrdude.conf" -v -patmega328p -carduino -PCOM11 -b57600 -D ebug.ino.hex:i"
avrdude: Version 6.3, compiled on Jan 17 2017 at 12:00:53
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2014 Joerg Wunsch
         System wide configuration file is 6.3.0-arduino9/etc/avrdude.conf"
         Using Port                    : COM11
         Using Programmer              : arduino
         Overriding Baud Rate          : 57600
avrdude: stk500_getsync() attempt 1 of 10: not in sync: resp=0x00
avrdude: stk500_getsync() attempt 2 of 10: not in sync: resp=0x00
avrdude: stk500_getsync() attempt 3 of 10: not in sync: resp=0xe0
avrdude: stk500_getsync() attempt 4 of 10: not in sync: resp=0xe0
avrdude: stk500_getsync() attempt 5 of 10: not in sync: resp=0xe0
avrdude: stk500_getsync() attempt 6 of 10: not in sync: resp=0x00
avrdude: stk500_getsync() attempt 7 of 10: not in sync: resp=0x00
avrdude: stk500_getsync() attempt 8 of 10: not in sync: resp=0x00
avrdude: stk500_getsync() attempt 9 of 10: not in sync: resp=0xe0
avrdude: stk500_getsync() attempt 10 of 10: not in sync: resp=0xe0
avrdude done.  Thank you.
Upload failed 

I see the board on COM11 as named "mEDBG Virtual COM Port (COM11)" on the Device Manager using Win64).  There is a light that blinks on the board several times when it is attempting.  There are no connections to the board other than the usb cable.  I am able to open the serial port on COM11 and there is a code pre-programmed on the board that echos serial port sends and it functions correctly.  I have tried the "AVRISP mkii" and "Atmel mEDBG" uploader options but the errors are the same.

Can you help me get the right upload settings?

Thanks.

EDIT:

I managed to program the board per the Atmel instruction sheet for the board:  http://www.atmel.com/Images/Atmel-42287-ATmega328P-Xplained-Mini-User-Guide_User... 
on pages 4 and 5.  It says: "select the connected mEDBG as Tool with Device as ATmega328P and Interface to ISP".  It worked, but I don't think the debugger is working.  The manual says:  " Click the "Project" tab and select the project "properties", click the "Tools" tab and select mEDBG as debugger and debugWIRE as interface."  but I don't see these options anywhere.  I see a dropdown menu for "selected debugger/programmer" but the only options are "Simulator" or "Custom Programming Tool", and then below the menu it says "Programming Only."  If I choose "Start Debugging and Break" under the AS7 Debug toolbar menu I believe it tries to upload to the board using the bootloader and fails to get a response.  This is the first time I've tried to use the AS7 programmer / debugger, I'm sure I've got something wrong!

If I choose "Atmel mEDBG" as programmer and "Always use programmer" I get the following output:

Uploading 'test_blink_debug' to 'Atmel atmega328pb Xplained mini' using 'Atmel mEDBG'
Uploader started for board Atmel atmega328pb Xplained mini
Uploader will use programmer name: medbg
.3.0-arduino9\bin\avrdude e\6.3.0-arduino9/etc/avrdude.conf" -v -patmega328p -cstk500v2 -Pusb ebug.ino.hex:i"
avrdude: Version 6.3, compiled on Jan 17 2017 at 12:00:53
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2014 Joerg Wunsch
         System wide configuration file is 6.3.0-arduino9/etc/avrdude.conf"
         Using Port                    : usb
Error during upload using programmer
Upload failed

         Using Programmer              : stk500v2
Upload failed
avrdude: usbdev_open(): did not find any USB device "usb" (0x03eb:0x2104)
The uploader returned an error
avrdude done.  Thank you. 

Ok that worked.  I think I had to enable the DWEN fuse for it to work because of an error it gave at first.  I put a breakpoint in, but I don't seem to have the option to step by one line at a time.  Also there was an error window that says that it doesn't support breakpoints.  Should this be working?

Yes I saw that note when I uploaded, I did have the cpp file with the ino name in the project folder.  When I select "Start Debugging and Break" then I get the "Device Programming" window.  Now I choose "Program" under "Memories" and there is no error.  I close the window.  Now there are 3 error notifications when it tries to start the debugger including, they are:  "Launch has failed and Studio could not read the target voltage.  Please check your connections and try again";  "Failed to launch debug session with debugWIRE.  This could be caused by reset line circuitry or disabled debugWIRE interface.  Make sure that the reset line is free before continuing.  Do you want to use SPI to enable the DWEN fuse?";  If I choose yes, then I get the last error: "Failed to enable DW:ispSetBaud: Unexpected response received:  Got 0x84, expected 0x1d" and the only option is to abort.

Ok thanks, I'm asking at the Microchip/Atmel forums.  One thing that is still in your realm, I think, is what happens when it is compiled in VM, and then debugged in AS?   

I read that VM combines all ino files into one ino file before compiling.  Does this mean it includes all the included library files as well?  For instance if I try to debug in AS7 is it going to just read through that one big file or is it going to jump into the separate library files that are used?

If you debug in VM, does it go into each separate library file that is used when it reaches a function from them or are all files combined into the one ino file?

Thanks.

Hi,

When you follow the instruction to make a project_name.cpp from your .ino and to have an empty project_name.ino in your project then you question about combining .ino files becomes irrelevant. The atmel debugger doesn't like .ino files so this is why visual micro supports the project_name.cpp alternative. 

Normally for arduino it is only the .ino files that get combined into a .cpp all other .cpp files in a project including core and libs remain as normal source code and will be compiled correctly.

If you click "vMicro>Show Hidden Files" then links to all libs will be included in the atmel project and the debugger will find them more easily. Click the menu again to remove the short cuts if you do not want them

"File>Open Arduino Project" is a Visual Micro menu item. I don't understand the question in your last post.

Thanks for the update