I've noticed at the games here at Georgia Southern University (I-AA) the crews (Southern Conference) have been using bright orange bean bags.  Trust me, there ain't no losing those things.  They stick out like a sore thumb.  
Here in GA, I haven't heard of any official word on which color to use.  Pretty mush everyone sticks with white.  I'm a BJ, and I take both out onto a field.  I use the blue for the PSK spot (wherever the kick was caught) and use the white for all fumbles/first touching.
And for the record, can I just stress how much it drives me crazy when I see refs bean bag an interception in HS?!