The quirks you're going to deal with really depend on what OS you're using, and what you're using it for. Remember, more details means better responses.
Yes, data and stuff is usually stored on an EBS volume with EC2, it allows you to keep versioned snapshots and easily resize storage space. As for installing packages (I assume you mean linux here), it's not that different from a VPS. You start the machine up, SSH in, and yum/apt-get install whatever you need, and it stays there until you shut the machine down. Now, if you're really going to be using it like a VPS, and wont be shutting it down, then you'll only need to choose your packages once, and forget about it.
If you do plan to shut it down and open a new instance however, you will lose everything on that instance store (that instance's hard drive, basically). Data and apps can easily be stored on a separate EBS volume, which is independent form the instance store, but I'm not sure how you would go about installing packages to what is basically a different drive.
As for resources to guide you, read the manual:
Sorry if my answers are a bit general, but you didn't really give me a lot to work with. Got any more specific questions?