Download the archive and extract it into a new folder.
When you run ModMerge for the first time, you have to select the game paths using the buttons at the top. Make sure that there are check marks on all three.
To combine two mods, you have to select at least a map and one database from the mod list. Mods near the top of the list have higher priority than those at the bottom.
The last step is to select a name for you new mod and click on the button at the bottom of the window.