I feel your pain. A couple of suggestions. First as Matty suggested, backup your data. Find out where your crucial apps store data, and make copies before you do your upgrade.
Second, consider using a system partition, and keeping as much of your crucial data as possible not only off that partition, but off that drive altogether. Windows loves to eat partitions on the same drive of the system partition it just ate.
If you use a system partition and keep as little data as possible on it (basically, stuff that gets put there automatically by Windows or other software), depending on what you have installed, you should be able to do a whole partition backup (Nova Backup, Acronis, etc) and keep the whole thing under 15gb. I keep the big installs like Photoshop off the system partition though, so YMMV.
Anyway, the point is to let Windows have as little fun as possible when it inevitably screws the pooch. This will limit any data loss to hardware failures, rather than Windows.
If you haven’t tried whole partition backups yet, you should. You can backup a partition in like 10 minutes, and it runs in the background. And you can restore just as quickly. One cool feature (at least of Acronis - I don’t recommend Acronis because of some of the newbie-unfriendly stupid choices the devs have made, but it’s what I’m familiar with and inertia has kept me with it so far) is that even if a partition backup won’t work with your new hardware setup, your data is still there. You can browse the backup file and dig up whatever specific data you want. I did this recently when my system went FUBAR and I couldn’t restore from a backup. A day or so of digging around and I had all my application data (including DS) back.
Protip: if your partition structure starts getting complicated (mine got a bit complicated; I have 6 or 7 HDDs and most of them are single partition, but my system drive has two partitions and another has 3 I think), write down which partition goes with which letter; Windows is not mature enough to handle persistent partition letters yet.