OK, sorry to confuse you. Since you are going on a trip this year, and presumably using some of the days on the 6-day pass that you are upgrading, then yes, the clock would start ticking on the day that you first used the 6-day ticket.
So let's say you arrived on the 18th, used a couple of days on your 6-day ticket, then upgraded. Your AP would start on the 18th of October, then be good through the 18th of October 2010. So for the remainder of this trip, you would have unlimited admission to all of the parks, then when you came back next September, your annual pass would still be good and you would have unlimited admission to all of the parks for that trip.
Most folks say that break even on an Annual Pass is about 12 days in the parks. So if you think you will spend more than 12 days in the parks over the course of the year, then upgrading to an Annual Pass will make sense.
If you are only spending a couple of days this year, and a couple of days for next years trip, then purchasing the non-expiring option on your 6 day ticket may be better.