I want to build a small board, with the 2009 micro, the crystal, the capacitor for power source stabilization, the needed circuitry (it's a flash trigger). I thought of soldering a 2 pin header, to "extract" tx and rx pins. Then I planned to eliminate the micro from an adruino board, plugging this latter board to my pc, connecting tx and rx to the corresponding pins of my little board, give power to the small board and...well, what I expect is that this will make possible for me to program the small board (which contains the atmel with the bootloader already burned).
I saw somewhere the same comfiguration without the cristal on the "slave" board. Is it possible with the crystal? I was thinking that maybe the serial com may go mad with two (unsicronized) crystals.
This would be useful also for debuggin purposes (I use the usb of the "mother" board to sniff data sent from my little board).
If it's not possible with 2 crystal the obvious solution is to add a jumper to eliminate the second crystal when not needed.
Apart from the strict question: any other thing to take into consideration?
Yes sure that will work. Don't worry about the 2 crystals.
You can run your small board without a crystal BUT the atmega chip that came with your arduino is set up to use one and won't work without it. You can get a plain atmega chip that would use the internal oscillator instead of the crystal but it would need a different bootloader.
Makes it very easy to make a homebrew board and program it without any fuss. I use one all the time. It behaves exactly like a real Arduino in use, complete with auto reset and USB power.
The RBBB instructions linked from this page gives you the low down.