This question has been asked numerous times over the last few weeks on multiple forums.
The answer is - you can apply the YE update anytime, regardless of whether or not you still have 2009 payroll(s) to process. The YE update does not include tax table updates for 2010. Those are part of the 2010 US Payroll Tax Update.
The 2009 YE update does include all previous YE updates, hotfixes, and service packs.