I'm looking to create an AWS system with one master EC2 instance which can create other instances. 
For now, I managed to create python files with boto able to create ec2 instances.
The script works fine in my computer environment but when I try to deploy it using Amazon BeanStalk with Django (Python 3.4 included) the script doesn't work. I can't configure aws cli (and so Boto) through SSL because the only user I can access is ec2-user and the web server uses another user. 
I could simply handwrite my access ID key and password on the python file but that would not be secure. What can I do to solve this problem? 
I also discovered AWS cloudformation today, is it a better idea to create new instances with that rather than with the boto function run?
This sounds like an AWS credentials question, not specifically a "create ec2 instances" question. The answer is to assign the appropriate AWS permissions to the EC2 instance via an IAM role. Then your boto/boto3 code and/or the AWS CLI running on that instance will have permissions to make the necessary AWS API calls without having an access key and secret key stored in your code.
How to create ec2 instances from another instance? boto awscli