Even if you don't plan on getting the VIP tickets with the assigned seats, get your general admission tickets ahead of time. POTC has been selling out weekends several weeks ahead (and weekdays too for that matter). I would not recommend you wait to get your tickets until the day of, POTC has been very popular at the El Cap because of the special displays and stuff.
To see if it's likely the show you'd want to see may sell out, go to the El Capitan site, to tickets and showtimes and click on the date you think you might go, pick a time, it will show you a mock up of the theater seating, you can roll your mouse over the differnt sections and see how many seats they have left, if it's less than 100 in the section you'd like to sit in, I'd say go ahead and get your tickets then.