Do I have to do a manual update, then root? Or root, then update?

Re: Do I have to do a manual update, then root? Or root, then upd

Just reflash ClockWorkMod and reflash Superuser, and in the future, if you're rooted, don't accept OTA updates.

I'm definitely a newbie and was wondering about doing the OTA update. I just got the notice today and was about to download it but decided to check on here first. . .
I'm rooted and backed up what can be with Titanium back up and My backup root. . .
So if I shouldn't do the OTA update, what should I do?
Shabbypenguin has a thread with a link to the new update on here but reading it, he states that he had a problem with a few apps. I was thinking that doing the OTA would prevent that and then root again. Is that wrong?