Pololu avr programmer with Arduino

I recently purchased a Pololu USB avr programmer v2.1 and am having some issues with getting it working. Using the SPI interface on two Arduino Mega clones I can bootload and then upload a sketch. However on two Nano clone boards I can only bootload them and uploading a sketch produces a error that they are not in sink and tries 10 times. Also how do I use the second header on the programmer the one with tx and rx pins.
Thanks for any help.

Hi Rowan,

The second header on the Pololu USB AVR Programmer v2.1 is the USB to serial (We have a tutorial on how to use USB to Serial ).

Are you using the correct bootloader and configuration for the Nano board? Are you able to give the specific error and any codes it provides?

I believe I have followed the above tutorial. However uploading code using the USB to Serial does not work, I can upload code directly onto the same Mega not using the programmer however with the programmer I have had no success. I am trying to press the reset button at the correct time however I am not sure how important the timing is.
The error is as follows:

avrdude: Version 6.3-20171130
Copyright © 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright © 2007-2014 Joerg Wunsch

     System wide configuration file is "C:\Program Files (x86)\Arduino\1.8.7\hardware\tools\avr/etc/avrdude.conf"

     Using Port                    : COM8
     Using Programmer              : wiring
     Overriding Baud Rate          : 115200
     AVR Part                      : ATmega2560
     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
     StabDelay                     : 100
     CmdexeDelay                   : 25
     SyncLoops                     : 32
     ByteDelay                     : 0
     PollIndex                     : 3
     PollValue                     : 0x53
     Memory Detail                 :

                              Block Poll               Page                       Polled
       Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
       ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
       eeprom        65    10     8    0 no       4096    8      0  9000  9000 0x00 0x00
       flash         65    10   256    0 yes    262144  256   1024  4500  4500 0x00 0x00
       lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
       signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

     Programmer Type : Wiring
     Description     : Wiring
     Programmer Model: STK500
     Hardware Version: 15
     Firmware Version Master : 2.10
     Topcard         : Unknown
     Vtarget         : 0.2 V
     SCK period      : 8.7 us
     Varef           : 0.0 V
     Oscillator      : Off

avrdude: stk500v2_command(): command failed
avrdude: initialization failed, rc=-1
Double check connections and try again, or use -F to override
this check.

avrdude done. Thank you.

An error occurred while uploading the sketch

Hi Rowan,

The timing of the Reset button is critical to getting the upload to work. I would play around with the timing and see if you can get it to work that way. Based on your error codes everything else seems to be working as expected.

Here is the full user guide for using this programmer. You may need to set it up with a utility prior to using it.