First you want to download the H2 Database Engine here: http://www.h2database.com/html/main.html
For windows there is an installer, for other operating systems there is a .zip
Windows
Linux:
Either way this opens the H2 console window in your default web browser.
Next go to the mods folder, and find the Pixelmon 2.5.7.zip.
RIght-Click select Extract Here or Extract to depending on how you unzip .zip files.
Then go back to the H2 Console in your web browser.
in the JDBC URl the box should say jdbc:h2:<path to>/.minecraft/mods/Pixelmon 2.5.7/pixelmon/database
Replace the <path to> with the location of the .minecraft/mods/Pixelmon 2.5.7/pixelmon/database folder. Or where ever you unzipped your Pixelmon zip. Because I am lazy I unpackaged it in the mods folder.
i.e. C:/<path to appData>, Roaming, .minecraft/mods/Pixelmon 2.5.7/pixelmon/database or home/<username>/.minecraft/mods/Pixelmon 2.5.7/pixelmon/database
username and password is blank.
You can now view Pixelmon's database, editing it requires you to know some commands and how to use the H2 Database Console. There is a cheat sheet and reference guide links in the side bar. At this link: http://www.h2database.com/html/main.html
After you are done editing, if the unpackaged folder is in the mods folder, put the .zip folder somewhere else just incase you mess up. Minecraft will run the unpackaged mod. So there is no need to repackage the file. If Minecraft doesn't run correctly rezip the assets and pixelmon folders in the Pixelmon 2.5.7 folder. Just because you can run it uncompressed doesn't mean you should. However, in terms of testing an unzipped folder will make testing changes a little quicker. IF you get fps issues (5 - 10 max) running pixelmon unzipped will increase to 15 -20+ fps. Make sure you have enough ram allocated to mine craft 2+ gigs should be fine (at 2 gigs there are some slight slow down issues with the options GUI). There are pros and cons, whatever you do is your choice.
Learn all you can. I am not responsible if you break something. This tutorial only showed you the tools, it is your responsibility to learn how to use them.