Hi Kimberly!
If you purchase a 1 day Magic Your Way base ticket and add the Water Park Fun and More option, you actually get 2 Water Park visits. What some will do is use one visit for an actual Water Park, and another for the interactive game experience at DisneyQuest.
If you plan to actually use those 2 visits, AND go to a theme park on your vacation, I'd say go with the base ticket and Water Park option. But if you only anticipate hitting, say, just one of the Water Parks, you'll come out cheaper paying at the Water Park gate.
Magic Your Way base ticket and Water Park option, at 2010 rates, is $136 per adult (or split up: $82 for park entrance + $54 for water park option).
Just paying at the gate is $46 for 1 day.
So you'll have to consider "most bang for your buck" based on what you plan to do when you arrive.
In any case, have as much fun as you can handle, and then have more of it :-)