There are a number of utilities you can use to preform backups.
fwbackups, Bacula, Rsync etc
AWS have some great security measures available to keep access to your AWS account safe.
AWS Multi-Factor Authentication (AWS MFA) provides an extra level of
security that you can apply to your AWS environment. With AWS MFA
enabled, when a user signs in to an AWS website, they will be prompted
for their username and password (the first factor – what they know),
as well as for an authentication code from their AWS MFA device (the
second factor – what they have). Taken together, these multiple
factors provide increased security for your AWS account settings and
If you're looking to build a scalable solution with AWS it's often a good idea to keep unique data (like your source code, website assets, server logs, uploads) outside of the EC2.
Furthermore, if you decide to go down the DevOps route and configure your EC2 through code you can do away with the need to backup an EC2 completely.
Everything from server configuration, server logs, code, uploads etc would live outside of the EC2s themselves.