How do you guys handle learning a new meaning for a character you've previously learned? When adding new characters, I've discovered that Skritter thinks I already know it fully, as I covered it in a different context.

I can only speak as a Japanese student (but there is a book by the same author for Chinese). I am studying using the Heisig Method in (Remembering the Kanji) RTK1. One of it's strengths is it assigns just one keyword to a kanji. Sometimes he has additional meanings but they are optional when creating your own mnemonics. Next I will study RTK2 which will cover just the Chinese readings then I will study for the JLPT and go for the Japanese readings.

Multiple readings and multiple meanings can turn learning Kanji into a mess. You may just want to focus on the first reading and meaning listed. Then latter learn additional meanings and readings as you come across them in the real world.

That's roughly been my approach until now (I've looked at some Heisig keywords but not used it properly).

But now I'm coming across significant secondary meanings, basic examples being:
-得 dei3 and 得 de5 are both very common
-the confusion between noun and verb form of 差
etc.

How would you suggests learning additional meanings using Skritter?

For me, the only way I learn the new meanings is in context. So a common character comes up in a text with new meaning, one my teachers explains it, and repetition and seeing it again again helps me internalize it.

Well, I would have a flashcard in Anki for the first meaning, and so I'd add a new flashcard for the new meaning. I'd also update my Skritter definition with this in account, and perhaps put in a second short example sentence from my flashcard...

I have a (Japanese) dictionary called the "Grand Century 2nd Edition" or something like that. When I learn a character like 受 (in this case as part of the verb 受ける) I look it up in the dictionary. Under this particular verb there's ten different meanings, with each meaning having at least 2 or 3 example sentences (with English translations). Reading these example sentences helps me see what all English words this verb can actually translate into, and in what situations it is used in real life. This works for all parts of speech (not just verbs), but I've found that in Japanese at least verbs tend to have the most disparate meanings compared to nouns or other types of words.

This gives me a context base to work from, but by itself it's not enough. To really remember some of the less-used meanings, I usually need to encounter them in the wild, either through reading or listening to T.V., etc.

Or here's a better example (I tried to put it in the same post, but there's some kind of bug on these forums that causes my browser to grind to a halt the longer I have this Reply box active...):

I originally learned 表　as a part of the verb 表す (あらわす：　to reveal; to express). Some time later, I learned the word 表　(おもて：　front; facing side). These two words have completely different pronunciations, and at first their meanings seemed to be unrelated. But, after thinking about it I realized that the side of an object which REVEALS itself to you as you look at it is the FRONT side, the side that is FACING you. So, in my head I fabricated a relationship between these two different words which have different pronunciations but the same 漢字. I don't care whether or not that relationship actually exists in Chinese or Japanese or anywhere else - as long as it helps me remember the words I really couldn't care less.

Looking at some of the other words that contain this character, I see some other pronunciations as well, such as 表情 (ひょうじょう：　facial expression). Again, I would try to build some kind of association between this meaning and the ones that I already know for this character.

Where it can get tricky is when the two meanings really do have absolutely nothing in common. You really have to get creative in those situations...sometimes brute force memorization ends up being the best bet in those cases, but I think you'll find that they are the exception rather than the rule. Most meanings are somehow related in concept, especially if you can stretch your imagination a little.

Thanks! I'll definitely look into the methods people have mentioned. I think just finding good example sentences and adding notes in the definitions on Skritter will help, also marking myself as wrong on the word if I don't get both definitions will bring it back into study on Skritter.

One thing that I found handy was like the "n(oun) before v(erb), c before s" rule for practice/practise in English. This applies to 差 cha1/cha4 (n before v, 1st tone before 4th tone). I'm not sure if this helps anyone who didn't know the rule in English though!