I would keep all the patches the same for OS and Unity until you get the second server up and running. Once you have it running, then go ahead continue with the updated patches. Some OS patches such as Exchange may be different and cause little issues. I would also on the new server, go for the Unity update SR releases and patches.
The Windows 2000 SP4 update on the Unity Microsoft download page, dated July 10, 2006, includes all of the previous patches. By the time you build your server, if Cisco has not updated this file to include the recent August patches, released August 8th, I would recommend going to Microsoft's site to get these. That way you will be most current.
I research each one before applying to the Unity server and also load on a test Unity server beforehand. For example, I do not apply security fixes for products that are not on the Unity server, such as Outlook Express. Applying certain hotfixes can add dlls to the OS that may impact Unity's functionality, specifically anything related to Outlook (since Outlook on the Unity server is not supported and can cause problems with MAPI to Exchange). I access Windows Update on Microsoft's website and select the Custom option. I then uncheck any patches I have elected not to apply. As always, I break the mirror set before applying anything to the Unity server as a precaution. Hope that helps!
The only ones I did not apply were KB920214 - Security update for Outlook Express and KB911567 - Cumulative Security Update for Outlook Express. If you go to website http://update.microsoft.com/microsoftupdate/v6/default.aspx?ln=en-us and click on Custom. Microsoft Windows Update will check your computer to see what updates are required. You may need to add the website to your trusted sites in Internet Explorer. Uncheck the Outlook Express updates I mentioned above. Then click Install Updates. As I mentioned earlier, break your mirror set so you have a way to recover quickly before applying the maintenance. BTW - The Microsoft Security Baseline Analyzer is supported software on the Unity server. On a DL380G3, 2CPU server, these updates took about 20 minutes to download and apply. We also use HP Insight Manager on our servers and this past weekend, I also upgraded the Insight Manager agent software to 7.51. Both require reboots, but you can defer the OS patch reboot until after upgrading the HP agent software, if that is something you want to do as well. If you have an IBM server, they probably have something similar for keeping the hardware revs current.
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