How-to upload program to MCU with flashed bootloader

Other Hardware 3rd Party Boards
1

How is it possible to upload application in hex format to Atmega328 with alredy flashed bootloader (original Arduino Duemilanove board)?
Is it necessary to use usip/avrdude? What is command syntax? Is possible to use tools like putty?
My device sending data over RS-232 to PC each minute. Is possible that user will overwrite program by mistake in ATmega328 over RS-232?

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martin159:
How is it possible to upload application in hex format to Atmega328 with alredy flashed bootloader (original Arduino Duemilanove board)?
Is it necessary to use usip/avrdude? What is command syntax? Is possible to use tools like putty?

Use avrdude. The syntax is shown if you enable verbose upload in your preferences.

martin159:
My device sending data over RS-232 to PC each minute. Is possible that user will overwrite program by mistake in ATmega328 over RS-232?

No.

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/tmp/app/arduino-1.0.5/hardware/tools/avrdude -C/tmp/app/arduino-1.0.5/hardware/tools/avrdude.conf -v -v -v -v -patmega328p -carduino -P/dev/ttyUSB0 -b57600 -D -Uflash:w:/tmp/build3646094179928330495.tmp/Blink.cpp.hex:i

Usage: avrdude [options]
Options:
  -p <partno>                Required. Specify AVR device.
  -b <baudrate>              Override RS-232 baud rate.
  -B <bitclock>              Specify JTAG/STK500v2 bit clock period (us).
  -C <config-file>           Specify location of configuration file.
  -c <programmer>            Specify programmer type.
  -D                         Disable auto erase for flash memory
  -i <delay>                 ISP Clock Delay [in microseconds]
  -P <port>                  Specify connection port.
  -F                         Override invalid signature check.
  -e                         Perform a chip erase.
  -O                         Perform RC oscillator calibration (see AVR053). 
  -U <memtype>:r|w|v:<filename>[:format]
                             Memory operation specification.
                             Multiple -U options are allowed, each request
                             is performed in the order specified.
  -n                         Do not write anything to the device.
  -V                         Do not verify.
  -u                         Disable safemode, default when running from a script.
  -s                         Silent safemode operation, will not ask you if
                             fuses should be changed back.
  -t                         Enter terminal mode.
  -E <exitspec>[,<exitspec>] List programmer exit specifications.
  -x <extended_param>        Pass <extended_param> to programmer.
  -y                         Count # erase cycles in EEPROM.
  -Y <number>                Initialize erase cycle # in EEPROM.
  -v                         Verbose output. -v -v for more.
  -q                         Quell progress output. -q -q for less.
  -?                         Display this usage.