I feel auto loading the extension is a bad thing, unless you really need to spawn sessions automatically.
The reason being is when there is a forced patch you can patch ones using the 'Default' option (or just loading the game outside of IS), and then continue to log in using the no patch option. Sometimes the extension will cause a CTD when there is a version conflict (before the new version is released). Loading it manually, you can still play under IS, use scripts that don't require the extension, and in general behave as normal until ISXEQ2 is updated.
Not everyone will agree with me on this point, but in my experience auto loading the extension causes more trouble than it is to type 'ext isxeq2' when you're ready to start loading scripts that require it.
Regarding Patches:
Any time there is a forced patch, I try to make a post as soon as I've confirmed the patch will be forced. I made a post on the 16th here:
http://www.isxgames.com/forums/showthread.php?t=1557
Most of the time when there is a forced patch we get a client version mis-match warning from the client. However on some occasions like last week, you can still log on, however the game is unplayable. We treat both conditions the same way.
You patch your game the day it is required, and you wait patiently for the new extension to be released.
If for some reason you are unable to patch the day of the forced update. You run the full patch update 'default' or via the normal loading method, then obtain the back dated everquest2.exe from the day you should have patched. This back dated everquest2.exe is generally available on twonk, and when it is not, you can usually get help on IRC. Doing the full patch is REQUIRED because often times there are many support, ui, and other files you need in addition to the exe file in order for the game to be stable.
I believe all of this is spelled out in the FAQ and on the Wiki, though the information may not be clearly consolidated.