Building a stepper motor controller

So i have successfully built a stepper motor controller using Arduino Uno and Nano. Now i am designing a PCB with Arduino on board using the schematic available on site. This will help me directly connect pins on board without any external wiring. Now my questions are :

  1. When i assemble the whole PCB, how do i burn the bootloader?
  2. Can I burn the bootloader using UNO board? or i have to get a programmer?
  3. I am going to provide USB mini or micro slot for programming by which i can program the board, can i use it for burning the bootloader?
  4. Kindly guide me stepwise after the assembly.
  5. Any suggestions are also welcome.

Thank You

  1. Can I burn the bootloader using UNO board?

Yes.

  1. I am going to provide USB mini or micro slot for programming by which i can program the board, can i use it for burning the bootloader?

No.

  1. Easy way: have an ICSP header on your board. Connect your programmer/Arduino as programmer to the ICSP pins, and select Tools:Burn Bootloader.
    Doesn't have to be a 2x3 header, can be 1x6, can be pads on the board, can be whatever you want as long as you can connect to SCK-MISO-MOSI-Reset and Gnd, and power if the board is not independently powered.
    SMD 328P type processor? Can even be an adapter that is pushed down on top of the chip, see below.
    Need a standalone programmer that you can load boards from a file on SD card? Got that too. This one lets select 1 of 16 programs, I also have a 2nd that supports 256 programs, and is also buffered for 3.3V target systems. Connect the P-ICSP header to the slave board, select the program, press Start. Can be battery powered even, with 3xAA battery pack for long life.
    Cross Roads Electronics

    http://www.hobbyking.com/hobbyking/store/_46316__Atmel_Atmega_Socket_Firmware_Flashing_Tool_US_Warehouse.html?strSearch=atmega

Wouldn't "How to burn the bootloader?" have been a better Title ?

I used this Tutorial successfully.

...R

thank you everyone for your suggestions, I can now go ahead with all your valuable inputs.