Open FOMM, click the Package Manager button. When the Package Manager opens up, click the Add FOMod button (you may have to select the option from the dropdown menu). Then browse to the zipped up FOMod and open it, say "yes" to the "copy file to FOMod directory" prompt, and wait a few seconds. It will show up on your list of FOMods. Highlight it and click "Activate". Seems like a lot of steps but it isn't really any harder than installing a mod the normal way, plus it comes with some cool features - easy uninstalls, version checking, file reordering, etc.