The Pearl download from the first link will upgrade you to 4.2.1.93. I see no reason why you shouldn't do it, though you don't necessarily have to. Alternatively, you could upgrade to 4.2.1.101 using the instructions found on this thread:
http://www.blackberryforums.com/gene...2-1-101-a.html
Either way, you should read through the entire first post on that thread, since it will tell you a lot about how the upgrade works and common mistakes you should avoid (the biggest one is not being patient and allowing the update to complete, which can take over an hour).
The second link is to upgrade Enterprise Server software, which is the software you would install on an email server if you were that server's adminstrator. You don't need any of that.
Doh...beaten by SECONDS...hey, at least I got all the info right.