You have a couple options for transferring files from a Windows to a Linux server.
One is to use Putty using the Putty Secure Copy client.
The other is to use WinSCP.
Both are documented here:
You'll want to first launch your instance, make sure your firewall (security group) rules are set appropriately to allow traffic on the appropriate ports and make sure your instance is assigned an Elastic IP so it is accessible from the Internet.
