I need to install Win98se onto an older PC I have, the thing is, will I be able to use windows update to make it secure (especially with recent events) or is it just too old?

The last time I tried windows update on a win98 pc, I dont remember it working.

WindowsUpdate works fine for 98se. I just updated the Mrs.' work pc yesterday, just use the "windows update" button in IE's tools menu, and await the deluge of updates.

Yes, works fine. You can also use the Windows Update Catalog (click Personalize and Show Catalog) to download all of the available patches for 98, 98SE, ME, XP, etc and save them to a CD.