Yes it is in the output it can't resolve build property {runtime.tools.arm-none-eabi-gcc.path}

Arduino 1.6.8 was only released this week so you will see that visual micro currently only supports up to 1.6.7

1.6.5 is good

Oh I have just noticed you are using an old version of visual micro. This will not work so well with arduino 1.6.6+. Arduino has changed a lot in the past year.

It does not matter that the arduino ide does not start. Visual micro does not use arduino.exe. So use the zip from arduino.cc to unpack 1.6.5 into a new folder such as c:\arduino\arduino165 then point visual micro to that folder.

No probs.

1)
If you want to stay with Atmel 6.2 and Visual Micro then you have to use an Arduino version 1.6.5 or earlier although it shouldn't be that hard to make a working hybrid by replacing the tools and/or core of an earlier version

2)
You point Visual micro to the location of the arduino ide folder so that it can find the sub folders for avr\tools\libraries and references. Also it can establish the version of the ide.

3)
In arduino 1.6.5 and earlier the arduino boards manager stored it's downloaded packages in a different location to 1.6.6+. This caused a lot of confusion and big difference that older versions of visual micro do not know. The path on your machine if different than I expect but maybe this is an XP thing. C:\Documents and Settings\Vaclav\Application Data\arduino15

On my machine:-

<= 1.6.5 board manager installs to "c:\users\myname\appdata\roaming\arduino15"
>= 1.6.6 board manager installs to "c:\users\myname\appdata\local\arduino15"

4)

Visual Micro allows you to have one ide of each different version installed at the same time. This means you can switch between 1.5 and 1.6 using the tool bar "micro apps list" combo box.

5)

No you can not update atmel 6.2 to work with 1.6.8 even if you paid for the software. 

Microsoft discontinued add-ins so visual micro was updated to use the newer system. I might try to revisit the backward compatibility for as6.2 and vs2010 at some future point but it's not easy and holds the project back from using more reliable newer and easier to support technologies.

Atmel in AS7 have also made the integration for arduino .INO more difficult (and more difficult to support) which is why Visual Studio is the main focus of Visual Micro especially now that it is free. The AS7 version is currently behind and will be updated during the next month or two but it will always be behind the VS version. For some users converting their arduino projects to .cpp in AS7 and working outside of the Arduino dev environment might be the best route forward.

I just tried 1.6.8 with the sam 1.6.6 tool chain in AS6.2 and it worked okay. 

However I had to install the sam tool chain using the Board Manager in the Visual Micro Explorer. This loads board definitions into a different location than 1.6.8

I suspect this is what the problem was when you tried it. If you used 1.6.8 to install the latest SAM defs then Visual Micro will not have found them and would have looked in the "old" location for them. Using Visual Micro to install the SAM hardware ensures the download is expanded to the correct location for Visual Micro. 

In essence, it doesn't seem to matter which Arduino Ide you use with Visual Micro but it is important to use visual micro (or arduino 1.6.5) to install the SAM hardware definitions so they are saved to the expected location. To install SAM 1.6.6 > Click the Yellow question mark on the Visual Micro tool bar then click the "Board Manager" tab. Then click Rescan or Restart Ide.

Ok. If yiou have as7 installed you don't need vm for your project. You can import your arduino project and it will convert it to a normal cpp project. Then you can 100% use asf

Tim, just FYI 
It looks as 1.6.8 is referenced correctly , but the compiler is still looking  for "manager" 1.6.4. 

I keep at it to see where is the issue, but you do not have to.
I am pretty happy running IDE 1.6.4. for now. 

Would this forum be OK to ask about using  "native USB" on Due ?
I had it working few years back using USBTask class. 
Now I want to use interrupts and having some issues. 
I cannot post on Arduino.cc they kicked me out for removing a post I got flamed for. And AVR Freaks do not want to talk ARM at all. 
Compiling 'ASCIITable' for 'Arduino Due (Programming Port)'
Build folder: /V.Micro/Arduino/Builds/ASCIITable/arduino_due_x_dbg
Summary: Header=1 Prototypes=3 Imports=0
Additional Defines: 
Architecture Tools: C:\Documents and Settings\Vaclav\Application Data\arduino15\packages\arduino\tools\arm-none-eabi-gcc\4.8.3-2014q1/bin/
Sketchbook: file:///c:/temp
Core Include Paths
Include Path 'C:\Documents and Settings\Vaclav\Application Data\arduino15\packages\arduino\hardware\sam\1.6.4\cores\arduino'
Include Path 'C:\Documents and Settings\Vaclav\Application Data\arduino15\packages\arduino\hardware\sam\1.6.4\variants\arduino_due_x'
"C:\Documents and Settings\Vaclav\Application e-eabi-g++" -c -g -Os -w -ffunction-sections -fdata-sections -nostdlib -fno-threadsafe-statics --param max-inline-insns-single=500 -fno-rtti -fno-exceptions -Dprintf=iprintf -MMD -mcpu=cortex-m3 -DF_CPU=84000000L -DARDUINO=168 -DARDUINO_SAM_DUE -DARDUINO_ARCH_SAM -D__SAM3X8E__ -mthumb -DUSB_VID=0x2341 -DUSB_PID=0x003e -DUSBCON -DUSB_MANUFACTURER="\"Unknown\"" -DUSB_PRODUCT="\"Arduino Due\"" "-IC:\Documents and Settings\Vaclav\Application Data\arduino15\packages\arduino\hardware\sam\1.6.4\system/libsam" "-IC:\Documents and Settings\Vaclav\Application Data\arduino15\packages\arduino\hardware\sam\1.6.4\system/CMSIS/CMSIS/Include/" "-IC:\Documents and Settings\Vaclav\Application Data\arduino15\packages\arduino\hardware\sam\1.6.4\system/CMSIS/Device/ATMEL/" -I"C:\Documents and Settings\Vaclav\Application Data\arduino15\packages\arduino\hardware\sam\1.6.4\cores\arduino" -I"C:\Documents and Settings\Vaclav\Application Data\arduino15\packages\arduino\hardware\sam\1.6.4\variants\arduino_due_x" "C:\Documents and Settings\Vaclav\Local Settings\Application Data\V.Micro\Arduino\Builds\ASCIITable\arduino_due_x_dbg\ASCIITable.cpp" -o "C:\Documents and Settings\Vaclav\Local Settings\Application Data\V.Micro\Arduino\Builds\ASCIITable\arduino_due_x_dbg\ASCIITable.cpp.o"
Build Core Paths: C:\Documents and Settings\Vaclav\Application Data\arduino15\packages\arduino\hardware\sam\1.6.4\cores\arduino
"C:\Documents and Settings\Vaclav\Application e-eabi-gcc" -Os -Wl,--gc-sections -mcpu=cortex-m3 "-TC:\Documents and Settings\Vaclav\Application _scripts/gcc/flash.ld" "-Wl,-Map,C:\Documents and Settings\Vaclav\Local Settings\Application Data\V.Micro\Arduino\Builds\ASCIITable\arduino_due_x_dbg/ASCIITable.map" -o "C:\Documents and Settings\Vaclav\Local Settings\Application Data\V.Micro\Arduino\Builds\ASCIITable\arduino_due_x_dbg/ASCIITable.elf" "-LC:\Documents and Settings\Vaclav\Local Settings\Application Data\V.Micro\Arduino\Builds\ASCIITable\arduino_due_x_dbg" -mthumb -Wl,--cref -Wl,--check-sections -Wl,--gc-sections -Wl,--entry=Reset_Handler -Wl,--unresolved-symbols=report-all -Wl,--warn-common -Wl,--warn-section-align -Wl,--warn-unresolved-symbols -Wl,--start-group "C:\Documents and Settings\Vaclav\Local Settings\Application  "C:\Documents and Settings\Vaclav\Local Settings\Application Data\V.Micro\Arduino\Builds\ASCIITable\arduino_due_x_dbg\ASCIITable.cpp.o" "C:\Documents and Settings\Vaclav\Application _sam3x8e_gcc_rel.a" "C:\Documents and Settings\Vaclav\Local Settings\Application Data\V.Micro\Arduino\Builds\ASCIITable\arduino_due_x_dbg/core.a" -Wl,--end-group -lm -gcc
arm-none-eabi-gcc*:error: C:\Documents and Settings\Vaclav\Local Settings\Application  No such file or directory
Error creating .elf

Thanks,
I sure appreciate your comments.