What are the sources of botch dice that you have to keep separate from other dice? I.e. you'd use different color dice in tabletop?
Weird Magic flaw is one.
Negative Faerie sympathies might be another (Serf's Parma) -- I remember they add botch dice, but I don't remember if you have to keep those dice separate.
Any others?
Looked it up. No, negative Faerie sympathy botch dice don't have to be kept separate.
So. Any other sources than Weird Magic?
Negative Faerie sympathies are the Devil. So you fumble while chewing gum and manage to break your arm because, ahem, there was this tiny bits of iron in the crack of the sidewalk.
Yes, I know they help a lot for faerie wizardry, but they always apply whereas the positive ones have a very limited scope. If a hailstorm would always come and help me blow a bigger bubble I wouldn't mind, but that's not the case.
So I'd go against RAW and keep them a different color to see if it's a drab accident (broken arm) or something that you may avoid by playing with faeries.