During the merge, you mustn’t try to edit the A and B buffers yourself. Emerge modifies them temporarily, but ultimately puts them back the way they were.
You can have any number of merges going at once—just don’t use any one buffer as input to more than one merge at once, since the temporary changes made in these buffers would get in each other’s way.
Starting Emerge can take a long time because it needs to compare the files fully. Emacs can’t do anything else until
diff finishes. Perhaps in the future someone will change Emerge to do the comparison in the background when the input files are large—then you could keep on doing other things with Emacs until Emerge is ready to accept commands.
After setting up the merge, Emerge runs the hook
emerge-startup-hook. See Hooks.