I assume you cooked your chicken thighs to 165–175°F (74-80°C) (depending on preference). 165°F (74°C) is the recommended temperature for safety (at least by US authorities), 175°F (80°C) is often recommended for texture (in legs and thighs; not for breast).
The best bet is to measure in several spots. You generally want to guess the thickest spot of meat, insert the probe past the center, then slowly withdraw it. How slowly depends on the response time of your probe. You then use the lowest temperature you see, especially if you see anything under the food-safety temperature (165°F or 74°C).
If there are multiple pieces of chicken, you should check several. Especially if they're different sizes.
Probe response times are anywhere from 20 seconds on fairly cheap thermometers, down to 3 seconds on expensive ones (like a Thermopen). 10 seconds is typical. You'll know its finished responding when the numbers stop changing quickly.
You also should rest the chicken, loosely tented, for at least 5 minutes (for just thighs, more like 15 minutes for a full chicken) after taking it off the heat—this lets the heat even out, and also will reduce the amount of juice lost when cutting.