I haven't had too much trouble with the guide
here (the same one Kingly_Krab linked to) and
here (same guide, two locations, different formatting, some minor updates to the second one). But the database setup information is incorrect for both of them because PEQ changed the way they handle database releases.
Basically, you can follow the guide for steps 1-3, and for steps 5+, but for step 4 you need to make some changes. Also, while you can download the quests files from the source given in the first guide (or at least you could back in late January), you can also get them from the PEQ database site (see below). I personally recommend using the PEQ site.
If all you want is the basic PEQ database (no bot support, and no private login server support), then you need to go to the new location for PEQ database dumps
here and download the database archive package. Unpack the package and you should have 5 files: eqtime.cfg, drop_system.sql, peqbeta*.sql, source_views.sql, and user_tables*.sql. If you have a prior database in place and you want to clear it, use the drop_system file, but for a brand new database you don't need it. The eqtime.cfg file should be copied into your server folder ("C:\EQ\EQEmuServer" in the guide). Then source in the peqbeta*.sql file and the user_tables*.sql file. I found with the 01/24/2014 release that both of them had a CREATE query for the spells_global table, and you only need one. This may have been fixed, but if not, it could throw an error or a warning depending on the way you source in the files. The source_views file will allow you to create view methods in your database. I don't think the views are required, at least I haven't run into any problems with not using them.
That should be all you need to set up a basic database for a public server, so you can move on to step 5 in the guide(s).
Now if you want to enable bots, and/or if you want to run your own private login server, then you'll need additional database tables that are not maintained by PEQ. To get these, for the time being at least, you need to retrieve the old database SVN just as the guide tells you to. But in this case, once you've retrieved the SVN you only need to source in the load_bots.sql and/or load_login.sql files. These will source in the additional sql files necessary to set up the database tables for those subsystems. You should not need to do any database updates.
Now if you want to run your own login server, you'll also need to setup table entries for the tbl* tables in the database, but I'm not going to go over that here, especially since I'm not sure my method is correct or best or optimal (although it does work).
Having never used VM-Ware, I can't speak to that question, but I hope the information above will help you get things working for a windows server setup.
Good Luck,
Drake Phoenix