upgrade from 4.1 to 5.0 (novice user)

hello,
I hope this is the right place to ask this question. (I couldn't find a
novice list) I am more of a programer than system admin, but we do what we
have to. I have just updated all the software on a win 2003 server, except
I couldn't figure out how to update MySQL, or more accuratly, I couldn't
figure out how to restore the data after a program update.
I found the following page (wasn't hard, it's on the download page :) )but
I'm having a problem following it. 
http://dev.mysql.com/doc/refman/5.0/en/upgrading-from-4-1.html 

these pages also seem relevant:
http://dev.mysql.com/doc/refman/5.0/en/windows-upgrading.html
http://dev.mysql.com/doc/refman/5.0/en/backup.html

I guess before I go any farther, the first question I should ask is should
I do this update. Is this new version important, or is it a case of, "If
it ain't broke, don't fix it"?

this server has about a dozen databases with around the same number of
database users.  
I tried to follow the instructions on the pages indicated above, with very
limited success. 
I find that much of the user documentation gives commands to be issued
from  shell>  (unix right?) and I'm not sure how this applys to windows.
Also instructions are given like "...do a LOCK TABLES on the relevant
tables...". Lock tables is a SQL command (right?) but from where? do I
need to write a script to do the backup, or do I issue the commands from
PhpMyAdmin or ...? any pointers on how to do this would be very much
appreciated.
please forgive errors on my part, I fought this thing till very late last
night  :)
Ray 



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