For QNAP, the recovery-mode feature is relatively new, so before you do a Debian install, make sure you're up-to-date with QNAP's latest firmware. You need to check that your QNAP NAS has at least v2.1.2 build 081114 firmware and you need to install the QPKG file that enables System Recovery Mode.
I'll try this out later in this article, but the Recovery process basically involves putting the NAS into a recovery state where very early in the boot process it stops and automatically uploads a new firmware image across the network from a TFTP server. So as long as you haven't somehow overwritten the boot-loader, this will allow you to revert back to QNAP's firmware, to a flash backup or to a fresh Debian installer image.
My guideline during this installation process was Martin's instructions here. The first step was to update to QNAP's latest firmware. Once I was up-to-date, I shut down, put a fresh hard drive in and reinitialized my system using the standard QNAP procedure. Since the Debian install process will make use of the network TCP/IP parameters, I made sure all were completely specified. Next, using the QNAP configuration pages, I turned on secure shell support for remote login.
The first step in the Debian install process is to log in via command-line in order to kick off the process. Installation is documented in Martin's instructions, which I won't duplicate here. But to get the install going, you're going to use a command-line on the TS-209 Pro to download three different components: a shell script; a Linux kernel; and a Linux disk image.
After the download, you'll execute the script to burn the other two parts to flash. When the burn completes, you'll be told to reboot the box. After the reboot is done, the installer will be running on the NAS, and you'll use ssh to log in and start the install.
Note that, for me at least, ssh complained about the identification of the TS-209. So I had to reset my secure shell "known hosts" file before I could continue. Once I had done this and logged in, the install was pretty much like any other standard Debian installation using a text-based menu (Figure 1)
Figure 1: Debian Install
To make life easier, the installer recognizes that you're on a TS-209 and will include all of the required components for this NAS. Since you're downloading all required components across the network, the faster your network, the quicker the install will be. For me, using a cable-modem, the whole process took a couple of hours and was mostly hands-off, except for a few prompts to set the root password, time zone, disk partitioning, type of usage, etc.