Using the most recent AWS CLI (http://aws.amazon.com/cli/) you can use the following commands to copy files from your Ec2 Instance or even your local machine to S3 storage.
aws s3 cp myfolder s3://mybucket/myfolder --recursive
You'll then get something like:
upload: myfolder/file1.txt to s3://mybucket/myfolder/file1.txt
upload: myfolder/subfolder/file1.txt to s3://mybucket/myfolder/subfolder/file1.txt
If this is your first usage of the aws CLI tool then you'll need to run:
This will ask you to enter your access key & secret along with specifying a default region.