Our exercise estimates are based on the adjusted MET values given from the Compendium of Physical Activities. These MET values are only for the time spent in movement.
When researchers are finding MET values, they are monitoring the athlete/participant for the duration of the activity. So, for weightlifting, that would be while performing the activity and during the rests between sets if it is an average time of rest between sets.
In other words, if you are taking an average amount of rest between sets, the MET values apply. If you're taking a really long rest between sets/reps, you may want to just include your "working time" in the calculations. For example, one study I found used 60 seconds between series of the same exercise, and 3 minutes between sets/exercises, so anything around there should be good!
With this information in mind, it then comes down to personal preference as to how you track this. The best way I can recommend to get an accurate Caloric reading from exercise is to monitor your heart rate with an activity tracker. We integrate with these trackers so you can be sure you are getting the best dedicated nutrition tracking software and also the best activity reading by a dedicated activity tracking software!
You can sync your wearable activity tracker with Cronometer by going to the Profile page and selecting the device you wish to connect.
As long as you are consistent in your tracking, you will be able to compare your results and data.