I am using Cloudtsack 4.0.1 with support for AWS. But can this be used to graphically manage AWS instances? So far I can use only EC2 commands which can be possible even with out Cloudstack.
No. "AWS support" means that CloudStack can be controlled using AWS API calls in addition to the native CloudStack API. However, the CloudStack GUI will only use the native API. Since the GUI does not use EC2 calls, it cannot control your VMs in AWS.