1. The usual order of installation for dual-boot systems (on a single drive) is other OS, then Linux. And you rely on the Linux bootloader, GRUB, for OS selection. I think it's possible to rely on Windows bootloader instead, but since recent versions of Ubuntu automatically setup the dualboot menu, relying on GRUB is easier.
Also, you'd ideally
leave the free space at the beginning of the drive for the Linux system partition (the beginning of a standard hard drive is faster than the end). But don't worry too much about it.
Ubuntu 9.10 also marks the switch to GRUB 2. I have only just started using it. I don't know much about configuring it, and I don't know if there are any dual-booting relevant bugs.
2. Hardware damage from Ubuntu (or any other OS) is almost impossible. And if you don't write files to your Windows partition, it's almost impossible for another OS to damage your Windows files.
As for netbook distros, Ubuntu Netbook Remix has the same hardware support as regular Ubuntu. Ubuntu Moblin probably is similar. Normal (non-Ubuntu) Moblin has very limited hardware support.
3. The GMA500 graphics chip in the Mini 10 has poor/mediocre Linux support. That's gonna be your main issue. ( You have a 10, not a 10v, right? If you have a 10v, it should be much easier)
You also might need a wired connection to download the wireless drivers. They're easy to enable, but I don't think they're on the CD.
As for tweaks, with 2GB RAM, if you don't need hibernate, I wouldn't bother creating a swap partition for Linux (the Ubuntu installer will tell you it's a bad idea ... ignore its warning