That's a neat idea.
Here's my recommendation. Assuming you use blue and red dice,
1. Fill in all "negative" pips with black sharpie
2. Fill in all "ignored" pips with red or blue sharpie to match the die.
That would make it look a bit cleaner, I think.
Yes, if you have the markers with matching colors at hand
What do you do about the crisis dice?
I use two standard dice; one with pips and one with digits.
And I have made a player aid with a crisis reference for the results of these two dice.
I'll upload my player aid in the files section of "BSG Express" soon.