5a. In the example on your right MRI will analyze the games played by Laser 1.7 and Ethereal 11.75.
5b. In case you Ethereal only MRI will produce the games between Laser 1.7 and all Ethereal versions.
5c. Leaving Engine two empty will act as option  and analyze the games of Laser 1.7 only. This option 5c is one of the better features of MRI, download the annotated games of CCRL and or CEGT of your latest version and get the results of all games played against all opponents.
6. Use All - will analyze all games in the PGN, not recommended because the setup of MRI is not based on that, the Phase Overview is not correct and the program is limited to handle 250 engines only.
1. As already stated MRI can only handle 250 engines, when a PGN contains more an error message will be the result.
2. PGN compatibility - MRI should work flawlessly with the PGN output of ChessBase, Arena and CuteChess. PGN from other sources may or may not work 100% reliable. The latter can be recognized by the remark on top of the HTM output:
PGN origin unknown.