i was wondering what everyone's opinions would be on encouraging single team play . Say all the alliance's would have a bonus resource ammount with no blue's marked , and marking one alliance blue would cut resource bonus . having a certain amount blues could even handicap team members resource's .

Absolutely not. This is a game of diplomacy. So you'd have to mark people friendly or hostile at varying points in the game (meaning some one friendly today, might be hostile tomorrow). Since diplomacy is part of the game, players shouldnt be punished for marking someone friendly. BTW, people could easily workaround this one. They could just avoid marking an alliance in any color.

^^