My understanding is that if you choose an AMI that does not have SQL server installed then you subsequently install it you must use the BYOL licensing model.
Also as yet I've not found an AMI provided by Amazon that that doesn't install SSAS, SSRS.
Depending on how many instances your planning on building you can always create an instance, configure it as you wish then create an image so you can create new machines from your own AMI. Alternatively code up a solution in powershell to reconfigure the install post initial creation.
We go with the former option.
MCITP SQL 2005, MCSA SQL 2012