Once you've got Mnemosyne installed, you need to add material to study. The best way to start is to use a collection of example sentences such as the Kanji in Context books.

Add examples sentences without furigana whenever possible (unless, of course, the furigana are printed with the word usually anyway).

For the answer, add the readings of any kanji you don't know and look up any words in a dictionary. Of course, if you use an electronic dictionary (my recommendations), you can save a lot of time and paste the definitions directly onto the card.

The most important point is to review your material every day.

Because it's easier to see what I'm talking about when you have a concrete example, I've uploaded a sample here.

To use this file, open Mnemosyne (make sure to use your existing .mem database), choose "File-> Import," and then browse for the file. In the browse dialog, you may need to switch the file type from XML to "all files."

Enjoy!