Uploading Hexfile to your arduino can be done using this application:

http://kmtronic.com/upload-hex-files-to-arduino.html

Uploading bootloader to your clean chip can be done like this:

http://arduino.cc/en/Tutorial/ArduinoISP

There is no need to use another ISP to get your chip working properly.

Uploading Hexfile to your arduino can be done using this application:

http://kmtronic.com/upload-hex-files-to-arduino.html

This is how you upload an Arduino Bootloader on an empty ATmega328 / ATmega328P-PU. Using an Arduino. (No need for a separate ISP Programmer).

From Arduino Uno to other Arduino Uno.

1. Open the ArduinoISP firmware (in Examples) to your Arduino board.
2. Select the items in the Tools > Board and Serial Port > Arduino Uno.
3. Upload the ArduinoISP sketch.
4. Wire your Arduino board to the target as shown in the diagram below. (Note: you'll need to add a 10 uF capacitor between reset and ground.)
5. Also connect TX from Arduino A to the RX of Arduino B and RX from Arduino A to TX Arduino B.
6. Select Target Board in Tools > Board > Arduino Duemilanove w/ ATmega328
7. Select programmer in Tools > Programmer > Arduino as ISP
8. Use the Burn Bootloader > Arduino as ISP command.
9. Go to Tools and Select Burn Bootloader. Done.

To upload on a breadboard without External clock.

1. Download: Breadboard.zip
2. Put boards.txt in your Arduino directory under Hardware > ATmega328. (For windows usually (C:/Program files/Arduino/Hardware/ATmega/boards.txt))
3. Close Arduino IDE and reopen it.
4. Open the ArduinoISP firmware (in Examples) to your Arduino board.
5. Select the items in the Tools > Board and Serial Port > Arduino Uno.
6. Upload the ArduinoISP sketch.
7. Hook pin13 from Arduino to pin19 on Chip
8. Pin12 from Arduino to pin18 on chip
9. Pin11 from Arduino to pin17 on chip
10. Pin10 from Arduino to pin1 on chip
11. pin0 from Arduino to pin3 on chip
12. pin1 from Arduino to pin2 on Chip
13. connect 5V from Arduino to pins 7 and 20 on chip 14, connect GND from Arduino to pins 8 and 22 on chip
14. Select Target Board in Tools > Board > ATmega328 on breadboard (8 MHz internal clock)
15. Select programmer in Tools > Programmer > Arduino as ISP.
16. Select Tools > Burn Bootloader. Done.

It's also possible with an Arduino Leonardo but you'll have to change some settings for that.

Note: You will need to put target board to Arduino Duemilanove w/ ATmega328 for programming the new chip (Uploading a code to it) instead of targeting Arduino Uno.