Well I write little character summaries that I add to over time. Just a separate word document, nothing elaborate. Just a general age range, occupation, nicknames, short description, and the longest part being the character history (which I write in short fragments rather than attempt to write it out like a story) This helps with back story. For example, one of my characters lost his wife in an epidemic. Then I realized that every character from the same city should also have lost someone in the epidemic. (otherwise its not much of an epidemic) So by the end of it, my poor main character had lost not only his wife, but 2 nephews, three nieces, a sister, a couple of in-laws, and an uncle, and everyone else had suffered similarly.
The index card system is simple, you just write the relevant information on an index card, which may or may not be color coded, then file them alphabetically. Or you could punch a hole in the corner and string them on a string or ring. I prefer to use the computer, because A. its harder to lose, and B. encourages you to look at them all at once, so you can see how they interrelate.