you need to change the indicators to clear ones, will look much nicer, i'll get a pic of mine and you'll see what i mean.
as for keys, they have rechargeable batteries inside, when they die, they die and need replacing.
you can do it yourself, but i tried and damaged the circuit in one so just got a local place to do the other and fix the one i damaged whilst opening.
costs about £20-30, but you will have to code it to the car.
if you search key coding for e46, you'll find instructions to do it.
you do need to code all keys at the same time otherwise you'll lose the non reprogrammed keys which is what has happened