You might have to do a search for how to tint a canopy. I have done the Ritt Dye method which involves using blue and black dyes and very hot water. Unfortunately I forget the ratios!
I know there is a thread here someplace with the correct colors, ratios and water temps listed.
You want to tint it BEFORE cutting it out of the extra flash sheet to prevent (hopefully) the canopy from warping. I have tinted the canopy already cut out and as still part of the sheet and still part of the sheet is the way to go. There WILL be some warping but it will be on the edges of the sheet not the canopy itself.
Found the thread I was looking for:
[link=http://www.rcuniverse.com/forum/m_3292832/anchors_3292832/mpage_1/key_tint%252Ccanopy/anchor/tm.htm#3292832]How To Tint A Canopy.[/link]
I used this method for the canopy on this Super Sportster 20.