You actually do have to do that when using USB. The User Guide has a good explanation of how to use Sync on your WiFi reader. See:
http://koboereader.com/user-guide
There comes a time when it begins to make sense to do a reinstall of XP. It takes a long time to get all the updates in place and you do have to do a good backup and reinstall software, but it is a weekend project that can have big rewards at the end in terms of how perky the machine is and how well it runs. Even the most careful person ends up with a messy registry and bits and pieces of leftover things stuck here and there. It's a day long project, for sure.
One of the work machines I did this to last weekend had not had a reinstall for about six years. It's still an underpowered computer, compared to my newish home computer, but it made a big difference. BTW, it doesn't take much to use Kobo on a computer. I can sync etc using a first generation Netbook with even less in terms of oomph than the computer I wiped and did a reinstall on over the weekend.