To start up with MultiWii, you need to download and install Arduino software first.
Download the MultiWii codes (MultiWii_dev_2013_07_15_r1539.zip) from Link below:
https://code.google.com/p/multiwii/downloads/list
Unzip it and then move the folder to the Ardunio libraries folder.
Open PDF guide below (Guide FC-EN-1.pdf) for more info how to start up.This guide is for MultiWii V2.0 and you can use it for V2.5 also.
If you have problem with Javaw.exe , go to Java webpage (Java.com) and download a free version of java and install it.
Now you should be able to run MultiWiiConf program. check following Youtube to learn 'how to use the configurator program':
http://www.youtube.com/watch?v=qT3MlyRvy9w
For how to set the MultiWii with configurator , read 'Newbies-Guide-to-Setting-Up-CRIUS-MultiWii-SE-board-v4-22-12.pdf' (you can download it at the bottom of this page).