Keep everything organized.

I have a main folder labeled something like Presenter Projects. Then in that folder I have a Source folder and an Output folder. Then each project gets a folder in the Source and Output folder. This way I keep all the files separate, and in one place.

On the Connect server, you just need to decide what folder the projects are placed in. If you only need to be the person with the server side management of the the presentation, then you can leave it in your "My Content" folder. Otherwise it would make sense to create a folder structure in the "Shared Content" folder to accommodate organized storage and management of the projects.