Here is a macro for Fusion that uses the RenderID and Coverage passes from V-Ray and combine them using color pickers for easy use. There is a default of 20 color pickers for 20 masks. I am quite happy and proud of it and use it in production myself.
Disclaimer: There are so many awesome tech guys out there and I am not one of them. So if you have any problems with them I am not sure how much I can help. I am also sure that it can be optimized quite a lot but I am not that good.
Please do me a favour, if you like the macro I would love to hear it on a quick email: email@example.com
Download *UPDATED* versions of the macro here:
http://www.thomasban...rIDs_v01_tb.zip (contains all four below)
http://www.thomasban...t_02_tb.setting (contains two color ID's)
http://www.thomasban...t_05_tb.setting (contains five color ID's)
http://www.thomasban...t_10_tb.setting (contains ten color ID's)
http://www.thomasban...t_20_tb.setting (contains twenty color ID's)
Download OLD VERSION here: http://www.thomasbanner.dk/download/fusion/macro/MultiColorIDs_v03_tb.zip