The three image components of merge are source 1, source 2 and the target image.
They can be scrolled individually by selecting from the drop down menu. There are short cut keys: "1", "2" and "b" for source 1, source 2 and target. (Obviously the target image contents are determined by the relative positioning of source 1 and 2)
A source image can also be scrolled by dragging with the right mouse button (RMB). The actual source moved depends on which source is selected from the drop down menu - either 1 or 2 (but not the target).
Question: Why allow scrolling with the right mouse button?
Answer: Well you can directly align one part of a source onto the other by a quick single stroke RMB diagonal drag.
Merge 2.4 has now made this feature clearer with annotation of the drop down menu.

Source images can be generated from a file, pasted from the clip board, pasted or written text, or software generated pattern. Either source when present can be over written at any time by one of the methods above. Irrespective of where they originated, each source (but not the target) can be positioned, rotated and scaled independently of the other source.

Merge must make a decision when a source image is replaced with another without the user explicitly changing the rotation and scaling settings of that source. It can leave the settings as is or automatically reset them to zero degrees rotation, default scaling and positioning. There are many cases where there is a need to try various images with the same orientation and size against a "fixed" image.

It has been decided in merge to leave settings unchanged when changing images to the same type such as file image to another file image. Rotation, scaling and positioning will only be reset to their default values when an image changes to another type.

Examples of change to an image include: pasted image to text; file image to software generated pattern etc.