I am fairly new to MM myself, but MiniLyrics is a plug-in. Therefore you need to install the .exe file for MiniLyrics to then extract the "gen_MiniLyrics.dll" which goes into the \MediaMonkey\plugins directory. The embedding script does quiet rightly go into \MediaMonkey\scripts\auto
The plug-in should then show up in Tools\Options within MM

I can't recall whether MiniLyrics does this for you, or if you have to do this manually

If this can help you more:
- Install MiniLyrics ( http://www.crintsoft.com ) for MediaMonkey. The latest versions of Miniyrics support MediaMonkey without you having to do special tricks. So best use the most recent MiniLyrics version.
- Make sure that MiniLyrics is set to automaticly start up with MediaMonkey.
- Install the auto-script (vbs) and the embedder (exe) in MediaMonkey's Scripts\Auto folder, like you already did.

If it still doesn't work, then:
- Make sure that MediaMonkey is running and the "Embedded MiniLyrics" dockable panel is visible.
- Make sure that MiniLyrics is running.
- Execute >>"C:\Program Files\MediaMonkey\Scripts\Auto\MiniLyrics Embedder Console.exe" embed<< (without >> and <<, using Start > Run)

Lyrics exist in
- "timed" or "scrolling" or "synchronised" version (those that scroll automaticly)
- "static" or "unsynchronised" version (those that have to be scrolled manually)

MiniLyrics has a lot of "synchronised" lyrics. That's why it's such a good and famous program. These lyrics contain timing codes that specify when each line of text starts.
Unsynchronised lyrics are basicly just text files, like the texts you can get from lyrics websites. Using MiniLyrics, you can "upgrade" these lyrics to synchronised lyrics.

Right-click MiniLyrics, go to "Skins", and choose a skin from the list. Available skins for iTunes are "iTunes", "iTunes6", "iTunes_5" and "iTunes_SBS".
You can also select "Have nothing on" or something else of course.
The colors, fonts, transparency, background image, ... can be chosen and saved/loaded from within the preferences dialog (Click MiniLyrics, press Ctrl-P, click left on "Lyrics Display").

I guess with "marked Song" -> Options-> Song Text you mean the song text (lyrics) you see in the song properties dialog.
MiniLyrics can be set to write lyrics to mp3 files in 3 formats (ID3v2 unsynchronised, ID3v2 synchronised, Lyrics3v2). I think the ID3v2's are enabled by default, and these can be read by MediaMonkey.

When you add new songs to MediaMonkey, the included lyrics are saved in its database. So when you externally change (or add) lyrics, MediaMonkey won't know about it, because it only looks at the information in the database, and not in the file itself (anymore). To make sure that MediaMonkey reflects the latest file information (like lyrics), rescan the music files, or use the "file monitor" functionality (in the Gold version).

If you do that, MediaMonkey will "see" the lyrics that MiniLyrics has added to the songs.

(It's also possible to let MiniLyrics write the lyrics to text files on your hard disk, and then use a MM script to read these and add them to the database.)

The "EvilTagger" script is probably what you want. It's for Evillyrics, but it should be easy to change it to work with MiniLyrics. But I don't recommend using this way, because the whole point of integrating MiniLyrics is that you can have all beautiful features of this nice program available, and you see scrolling lyrics for almost every song you play (if you enable this).
I only see a possible advantage of your request if you e.g. would like to search with MediaMonkey within song's lyrics. Then the lyrics really have to in the MediaMonkey database.

The script only embeds MiniLyrics ("external" program) into MediaMonkey.

You can set MiniLyrics to automaticly write the lyrics to mp3 using its settings.
Click on MiniLyrics and press Ctrl+P, or alternatively right-click MiniLyrics and choose Tools > Preferences...

Once you're in the options dialog, click on "Lyrics Download" in the left pane. Then, in the right pane you can choose whether to (and how to) automaticly download lyrics, and in which mp3 tags it has to save the lyrics (ID3v2 unsync'ed, ID3v2 sync'ed, Lyrics3v2).