Hi welcome to the forum.
The disappearing taskbar icons is a common Windows XP bug. If you haven't upgraded to Service Pack 2, it does go some way to helping out with the problem, althought it doesn't get rid of it entirely. It is caused (at least in part) because Windows boots up faster than it can place the icons for some odd reason. So if you have your computer automatically logging on to Windows, try making it so you have to enter a password. Wait until the hard drive has stopped grinding before you put the password and press return. This usually slows it down enough to ensure that most of your taskbar icons appear, although it's still very hit and miss.
Aside from that there's little that you can do. I for one have a laptop where the battery icon almost never shows, which is as irritating as hell when you want to know how much power you have left.
As for the IDE controller, if it came disabled you can probably leave it that way, unless you want to add something later on. Or put it like this, if something doesn't work with it disabled then enable it. It might use up a bit of resources enabled and slow down your boot time very slightly but aside from that there's really no difference.
