Progressing in Your Studies of Japanese with Mnemosyne

Mnemosyne is a powerful tool, but your memorization will proceed fastest if you do it in an orderly way. Here are my best tips:

1. Avoid romaji. If you feel like you need romaji, stop using Mnemosyne and practice your kana until you don't need them anymore. If your goal is fluency, you'll never make it with romaji. You need to be at the kana level before it even makes sense to start studying long-term using a program like Mnemosyne.
2. Avoid furigana whenever possible. If you're learned the reading of a kanji, don't use furigana. If you have to enter furigana because you don't know the kanji yet, that's fine, but once you learn the reading make sure you edit the card and erase the furigana (or move it from the question part to the answer part). You will not learn to read kanji well if you rely on the furigana.
3. Move from your native language's definitions to Japanese definitions as soon as possible. This also helps eliminate mistakes, as in having a definition like "score." Is it "score" as in "score points," "musical score," "score with her"? If you have a Japanese definition, it will also help you find synonyms and antonyms.

The gist of it is that you should move to all Japanese as quickly as you can.

If you haven't seen it already, you might be interested in how I passed the 2kyuu using SuperMemo, which is the program I used before I found Mnemosyne.