When you create your EC2 instance you have an option to create a new key pair.
Create a new key pair and download the key.
You can then import the private key directly into FlashFXP. You do not need PuTTYGen..
(You will only enter the private key, leave the public key field blank)
On the Site Manager make sure you enter the username as "ec2-user" or whatever the distro you installed uses as the default username.
I included some screenshots below
