Supermemo (And other programs that seek to accomplish the same purpose) creates within the user a very interesting way of thinking. (I recall reading this on the Supermemo site, but I forget where) When you encounter a concept that you do not understand, the simple solution is this: Throw relevant incremental reading material at it. Decode the material into flashcards, and retain with Supermemo. If you still find some gaps in your knowledge, simply throw more incremental reading material into Supermemo.
A policy of many institutions is to simply "throw money at" potential problems (Illegal drug trade, problems in the education system, etc.). In that same way (But with greater success than institutions), when you encounter ignorance with yourself, simply throw incremental reading material at Supermemo, and over time the ignorance will go away.
This philosophy of progressive and never-ending learning is very appealing to self-learners because it makes knowledge gaps less intimidating. Too often people are embarrassed to admit to a gap in their knowledge, so rather than try to bridge the gap, they simply don't acknowledge or do anything about it. I think this reaction can be partly attributed to the anticipation of the critical "You mean you didn't know that!?" sort-of response that I frequently hear from others. I hate it when I hear others criticize unintentional ignorance. Willful ignorance is another story, but if someone doesn't understand something, rather than focus on the gap, I prefer to take action in order to fill the gap.
So if you are ignorant about a subject, your response should not be "I don't know about that." Rather, it should be "I don't know about that YET."