1) I always use block colours and put 20 points in it at the start, occasionally i put 20 in bloodbound and unlock that.
2) I know as far as efficiency goes having an amp every 5/6 is mathmatically the best, but i prefer to use 1 tower with 8 amps around it, having the tower gem 2 grades above the amps. Plus bonuses are better with using multiple low level amps then a few high levels ones.
3) Sell them unless you get a red/lime combo, cause that one absolutly kills everything, but leveling them is expensive. If you sell it you get a decent amount of mana to unlock a gem you like using or more mana to buy gems and towers to start.