Back up, syncing issues

Hi everyone, I recently bought the iPhone 5S, I also have previous version iOS devices and they sync perfectlly with my itunes. So,

Q. 1

I decided to sync my new iPhone 5S with my itunes but every time I sync it, it does not transfer apps from iphone to itunes by itself, I have to manually do it from file->devices->transfer purchases. How can I fix this so that whenever I sync, purchases are automatically transferred as they are being done in previous devices?

Q. 2

In iTunes, I see 2 backup options, isnt the backup same as it is sync? Also, there is an option of automatic backups? When does it take automatic backups?

I have these few confusions, If someone can help me out, I will be really thankful. Thanks.