I agree it is confusing.
Daniel Petri has some very valuable suggestions on his site:
Be sure to find all the suggestions he has made about Hotfix management:
Windows Update
Windows Update Problems
Info Collected by Windows Update
Configure Auto Windows Update
Microsoft Software Update Services (SUS)
GFI LANguard Network Security Scanner
Microsoft Baseline Security Analyzer v1.2
HFNetChk
Shalvik HFNetChk Pro/LT
Microsoft Security Bulletins
Note: Some items might fit into 2 or more categories, for example IIS 5.0 and Windows 2000 updates, but they only appear in one. Also, many IE and IIS hotfixes were incorporated into Windows 2000 Service Packs 3 and 4 and into Windows XP Pro SP1/1a. Read the Windows 2000 SP3 Info, Windows 2000 SP4 Info, Windows XP SP1 Info and Windows XP SP1a Info pages for more on this subject."
These three topics discussed on his site:
Microsoft Baseline Security Analyzer v1.2
HFNetChk
Shalvik HFNetChk Pro/LT
I hope will improve matters for you. Poke around Daniel's site under this issue, as he writes very plain english description of the tools available, how to use them, and why.
If your update logs show a specific error message, please post it an that would help a great deal to resolving the issue.
One site I have often referred users to, that I think is very well done (but slightly long):
Please post again if the above does not resolve the issue. It is a resolvable issue.
Bill