I also keep the swamp cooler going throughout the entire duration of fermention. The first 3 or 4 days are really the only time you need to keep a watchful eye on it. After that, the water just insulates the carboy and keeps temperatures consistant.
I use the thermometer on the side of my carboy to guage the temperature. I also leave a floating thermometer in the water on the outside. I think this setup helps me figure out how much the temperature will drop when I add another ice bottle. The water generally cools to about 3 or 4 degrees below the carboy temp when I add an ice bottle, then slowly warms up to the wort temperature over time. Once the two have been even for a little while, I know it's time to add another bottle before the temperature in the carboy begins to change.
I think it's a safe bet to use the thermometer on the carboy (as long as it isn't submerged in the water,) especially during the first few days of fermentation because the yeast will constantly stir the wort as they move around. This should result in a nearly uniform temperature througout the carboy.