I don't know what to add to what you already know from the several other sources you have used asking about this. The CD/DVD restore I used restored it exactly like the factory setup. Expect the OS to be in the right place with full use of both drives.
I found this note which is probably what you are mentioning. "For models with 2 SSD, the bootscript will also format the 2nd SSD to Linux ext3 filesystem and assign a volume label of "HOME" to it. Then the system will mount it to /home at bootup (by seeking volume label). However, what the bootscript does is to look for a non-removable bit in the controller firmware of the 2nd SSD (/dev/sdb). People have reported that after they installed winxp or even ubuntu in their EeePC, the removable bit in the 2nd SSD will be changed to "removable", and the bootscript will think it is a hot-pluggable removable disk and will fail to format it and assign the correct volume label. Then they ended up losing the 16GB 2nd SSD (not automatically mounted by the system)."
I suggest you put in your Linux restore DVD and just do it. No problem and your free. But, *only after you experience a problem* go into the second SSD and figure out the problem. I have an Asus with just one 16GB SSD which runs Linux off a SD card so can't tell you much more than that.
edit: Well, yes I can. It wouldn't hurt for you to learn more about your computer by reading up on it at the
ASUS support site. Following directions exactly is a good skill for staying out of trouble.