Usually, images are captured with the camera on a stable tripod. Camera settings should be chosen so that you get well-exposed and well-focused individual images. If there are really bright objects in your composition, you might want to underexpose compared to what you would normally do. This is because the stacking will reduce noise, allowing you to recover more details in the dark, and by reducing your exposure you might be able to avoid blowing out some bright object, thus holding more detail in the bright areas. All images must be exposed identically. If your goal is minimum noise or maximum motion blur, then the camera's minimum ISO should be used to get a longer exposure. Using a polarizing filter may help not just because it can reduce glare--it is also a neutral density filter with a value of about 2 stops, allowing a slightly longer exposure. It is important to capture RAW files to maximize the amount of information available to Long Exposure Stacker.

The number of images required and the frequency at which they are captured depends on the subject. For small waterfalls, the water moves quickly relative to the distance the water falls, so 20 exposures captured at 1 second intervals or even faster works well. For large ocean waves hitting a beach once every 5 seconds or so, more images are needed (I have been using 50 to 60 but more would be better) and the images should be captured more slowly (5 seconds between images seems to work well for me). Also, with the larger, slower waves, having a longer exposure time helps a lot. 

It is also possible to capture short bursts of images hand-held. To do this you will want to use a fast shutter speed and likely a high ISO. If you are capturing hand-held, then during processing with Long Exposure Stacker you will need to use the optional alignment. I have seen this technique used to soften waterfall images captured with an iPhone 7 and low-noise images of interiors of cathedrals where neither flashes nor tripods are allowed.

Capturing Dark Frames 

With Long Exposure Stacker Version 1.5 and later, if you are taking images under dark conditions, you might consider capturing some dark frames. Dark frames can be used to reduce fixed-pattern noise, that is, noise that tends to be consistent from frame to frame, such as hot pixels and glow around the edges of the sensor. To capture dark frames, put the lens cap on and shoot 10 frames with the settings you just used. Do this just before or just after you capture your light frames. Some cameras with really low-noise sensors might be able to save time by only capturing 5 dark frames. If your camera has a particularly noisy sensor, you might want more than 10 dark frames. If your lens cap does not fit tightly you might have to cover you camera with a dark cloth. It is important to block all light from reaching the sensor.

With versions of Long Exposure Stacker before Version 1.5 I recommend that most users not use dark frames.

Flat-Field Frames

Long Exposure Stacker can use flat-field frames to correct for vignetting and some other lens artifacts. The vignetting correction can give better results than image processing tools like Adobe Lightroom. See Preparing Master Flat-Field Frames.

Preparing Images for Long Exposure Stacker

Long Exposure Stacker accepts images in many RAW formats and TIFF files. Some reasons on why you might prefer one over the other, and instructions for converting the RAW format images to TIFF, are here Preparing Images for Long Exposure Stacker.