I'm using Atmel Studio 6.2, Arduino IDE 1.0.r-r2, the last beta version of visual micro (1403.31).
The board is a Sparkfun pro micro 5V.
With the Arduino IDE everything is working like is the books, (compile, upload).

With AS 6.2 and Visual Micro, unable to upload to the binary via the USB bootloader. I get the following output message:

Binary sketch size: 6244 bytes (used 22% of a 28672 byte maximum) (0.30 secs)
Uploading to I/O board using 'COM16'
Upload failed. Did you select the correct upload method for this board?
Object reference not set to an instance of an object.

The command used is Project/Upload Last Sketch Build, not the Upload using Programmer.
After digging in every menus, preferences or other options, I did not find how to select the correct upload method for this board.  
Any help would be very welcome and appreciated.

Thank you for your answer but I tried every commands, green arrow , the green arrow with small dashes, which correspond to debug/start without debugging or ctrl-Alt- F5 or debug/start debugging or F5, I get always the same result.

Here is what I get with verbose on:

Compiling 'blink' for 'SparkFun Pro Micro 5V/16MHz'
Build folder: file:///C:/Users/Gil/AppData/Local/VMicro/Arduino/Builds/blink/promicro16
Summary: Header=1 Prototypes=3 Imports=0
Additional Defines: VISUALMICRO_COMPILER_VER=1;
Architecture Tools: C:\Program Files\Arduino\hardware\tools\avr\bin\
GCC: 4.3.2
Sketchbook: file:///E:/Electronics/Arduino
Include Path 'C:\Program Files\Arduino\hardware\arduino\cores\arduino'
Include Path 'C:\Program Files\Arduino\hardware\SF32u4_boards-master\variants\promicro'
Include Path 'C:\Program Files\Arduino\libraries'
Include Path 'C:\Program Files\Arduino\hardware\SF32u4_boards-master\libraries'
Include Path 'E:\Electronics\Arduino\libraries'
C:\Program Files\Arduino\hardware\tools\avr\bin\avr-g++ -c -g -Os -fno-exceptions -ffunction-sections -fdata-sections -Wall -mmcu=atmega32u4 -DF_CPU=16000000L -MMD -DUSB_VID=0x1B4F -DUSB_PID=0x9206 -DARDUINO=105 -I"C:\Program Files\Arduino\hardware\arduino\cores\arduino" -I"C:\Program Files\Arduino\hardware\SF32u4_boards-master\variants\promicro" -I"C:\Program Files\Arduino\libraries" -I"C:\Program Files\Arduino\hardware\SF32u4_boards-master\libraries" -I"C:\Program Files\Visual Micro\Visual Micro for Arduino\Micro Platforms\default\debuggers" -I"E:\Electronics\Arduino\libraries" -o "C:\Users\Gil\AppData\Local\VMicro\Arduino\Builds\blink\promicro16\blink.cpp.o"  "C:\Users\Gil\AppData\Local\VMicro\Arduino\Builds\blink\promicro16\blink.cpp"  -DVISUALMICRO_COMPILER_VER=1
C:\Program Files\Arduino\hardware\tools\avr\bin\avr-gcc -Os -Wl,--gc-sections -mmcu=atmega32u4 -L"C:\Users\Gil\AppData\Local\VMicro\Arduino\Builds\blink\promicro16" -o "C:\Users\Gil\AppData\Local\VMicro\Arduino\Builds\blink\promicro16\blink.elf" "C:\Users\Gil\AppData\Local\VMicro\Arduino\Builds\blink\promicro16\blink.cpp.o" "C:\Users\Gil\AppData\Local\VMicro\Arduino\Builds\blink\promicro16\core.a" -lm
C:\Program Files\Arduino\hardware\tools\avr\bin\avr-objcopy -O ihex -j .eeprom --set-section-flags=.eeprom=alloc,load --no-change-warnings --change-section-lma .eeprom=0 "C:\Users\Gil\AppData\Local\VMicro\Arduino\Builds\blink\promicro16\blink.elf" "C:\Users\Gil\AppData\Local\VMicro\Arduino\Builds\blink\promicro16\blink.eep"
C:\Program Files\Arduino\hardware\tools\avr\bin\avr-objcopy -O ihex -R .eeprom "C:\Users\Gil\AppData\Local\VMicro\Arduino\Builds\blink\promicro16\blink.elf" "C:\Users\Gil\AppData\Local\VMicro\Arduino\Builds\blink\promicro16\blink.hex"
Binary sketch size: 6244 bytes (used 22% of a 28672 byte maximum) (0.50 secs)
Uploading to I/O board using 'COM16'
Upload failed. Did you select the correct upload method for this board?
Object reference not set to an instance of an object.

Yes sorry, Arduino IDE is 1.0.5-r2
Upload using programmer is unticked
and the link to the board https://www.sparkfun.com/products/12640
The Arduino addon for the board is installed, an working properly  (it does not work with Arduino 1.5 IDE directories are different)

Yes, I can select the board with the associated COM port, the compilation works. 
I can upload the code using the hex file and  a standard ISP programmer (AVR ISP and some wires soldered on the board).

With the Arduino IDE I can upload the code using the usb bootloader, (AVRISP does not work  from Arduino IDE, it needs a different driver)

No, its blank

Uploading to I/O board using 'COM16'
Upload failed. Did you select the correct upload method for this board?
System.NullReferenceException: Object reference not set to an instance of an object.
   at processing.app.debug.AvrdudeUploader.uploadUsingPreferences(String buildPath, String className, Boolean verbose, Boolean ProgrammerUploadUsing, String mcuProgrammerOverrideName)
   at processing.app.SketchEditor.Upload(Boolean verbose)

The link has been refreshed with an update. There are new uploader messages when verbose compile is enabled.

Please post the trace again

Thanks

Here is what Aeduino IDE is doing :

Binary sketch size: 6,244 bytes (of a 28,672 byte maximum)
Forcing reset using 1200bps open/close on port COM16
PORTS {COM1, COM16, } / {COM1, COM16, } => {}
PORTS {COM1, COM16, } / {COM1, COM16, } => {}
PORTS {COM1, COM16, } / {COM1, COM16, } => {}
PORTS {COM1, COM16, } / {COM1, COM16, } => {}
PORTS {COM1, COM16, } / {COM1, COM16, } => {}
PORTS {COM1, COM16, } / {COM1, COM16, } => {}
PORTS {COM1, COM16, } / {COM1, COM16, } => {}
PORTS {COM1, COM16, } / {COM1, COM16, } => {}
PORTS {COM1, COM16, } / {COM1, } => {}
PORTS {COM1, } / {COM1, } => {}
PORTS {COM1, } / {COM1, COM18, } => {COM18, }
Found Leonardo upload port: COM18
C:\Program Files\Arduino\hardware/tools/avr/bin/avrdude -CC:\Program Files\Arduino\hardware/tools/avr/etc/avrdude.conf -v -v -v -v -patmega32u4 -cavr109 -P\\.\COM18 -b57600 -D .hex:i 

avrdude: Version 5.11, compiled on Sep  2 2011 at 19:38:36
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2009 Joerg Wunsch

         System wide configuration file is "C:\Program Files\Arduino\hardware/tools/avr/etc/avrdude.conf"

         Using Port                    : \\.\COM18
         Using Programmer              : avr109
         Overriding Baud Rate          : 57600
         AVR Part                      : ATmega32U4
         Chip Erase delay              : 9000 us
         PAGEL                         : PD7
         BS2                           : PA0
         RESET disposition             : dedicated
         RETRY pulse                   : SCK
         serial program mode           : yes
         parallel program mode         : yes
         Timeout                       : 200

Apparently, the forced reset is not completed with visual micro and the board does not switch to the bootloader on PORT 18

The elf and hex in the specified project output folder is a new feature. please switch on "tools>options>visual micro>compiler>show build folder" this will give you a link to the real build folder.

When the elf files are of the wrong time please compare with the ones on the build folder and let me know if they are different.

Thanks