That A and D saddle are far too high, the D in particular. To adjust the height on them you use the two allen screws either side of each string (there should have been a small allen key that came with the guitar), turn CCW to go down and CW to go up. What I do to adjust the height is adjust them down until the string just starts to buzz on the frets at normal picking force, then raise it until there's only the slightest hint of buzz when picking very hard, a bit harder than the hardest you would normally play.
- Before adjusting a saddle, make sure the corresponding string has been slackened, then re-tune and test, do this as many times as necessary until the proper height is achieved.
- You have to turn one screw each side of the string you're working on about half a turn at a time, then do the same for the screw on the other side of the string, it's important to try and keep the saddle reasonably level side to side (so that it's not tilting over), when you've finished adjusting a string you want the saddle to be fairly level (side to side, not back to front).
- Do each string in turn, starting at the low E (thickest) and working up to the high E (thinnest), it's no use just doing one or two, you want them all adjusted so they are just starting to buzz under heavy picking.
I'm terrible at describing things, so if any of the above makes no sense don't be afraid to ask for clarification.