You can also jump to marker A or B using the Go→Go to Marker A or Go→Go to Marker B menu entries.
Marker positions are also displayed at the bottom of the screen, under the Selection section:
Obviously, marker A can't come after marker B. If you try to set marker A to a frame after marker B, Avidemux will set marker B to that point, and marker A to the frame after where marker B used to be.
You can save part of a stream by going to File→Save→Save Video. Every frame from marker A to marker B will be saved, excluding the frame at marker B. Mathematically speaking, the set of frames saved is [A,B).
The Edit→Delete menu entry will remove frames from [A,B) from the stream. It can be used, for example, to remove commercials from a video capture. Avidemux will make sure to keep the audio in the stream in sync with the video, unless you have an external audio source.
This section only applies when video is in copy mode (encoder is set to Copy). In process mode (an encoder is selected for encoding), Avidemux internals ensure everything is alright.
Usually, each frame of video isn't that different from the one before someone's mouth moves a bit, the background shifts around, etc. Most video codecs use this fact to save space, by saving a complete frame every few seconds, and making the other frames simply a modification of the reference frame. Complete frames are referred to as Intra frames, or sometimes I-frames or keyframes.
Markers don't have to be at key frames, so your stream might look like this:
Where lowercase letters are intermediate frames, A and B are marked frames, and I is an intra frame. When you cut frames [A,B), you will end up with:
Where frames jkl are broken, because they specify changes relative to an I-frame that no longer exists. There are two ways of dealing with that:
Frames can be copied and pasted by doing Ctrl-C and Ctrl-V. When copying, you must make sure the first frame you copy is an I-frame; when pasting, the frame after the insert point must be I-frame.
You can confirm the start and end edit positions the frame displayed at the bottom of the screen, under the Selection section:
4. The Edit→Delete menu entry will remove frames from [A,B) from the stream.
5. Save the video with the section deleted. You can use the menu File→Save→Save Video. You may be able to use Video Copy and Audio Copy modes to do this edit, but you may not and you may have to encode the video.