The intent with Intervals is to track the client facing total as opposed to an internal cost total and Intervals is light on accounting functionality in general. There is not a way to enter a cost rate and a client facing rate at this time. Data can be exported and the rates modified to apply the costs to get profitability. That being said, if the hourly rates are not being billed to a client, or tracked in a client-facing manner, the hourly rates could be used to track labor costs instead. We have seen a few customers do this and it basically inverts the functionality and makes all of the reports cost centric instead of revenue centric. You can use work types that are the person and their rate/cost per hour or the type of work they do and the rate/cost.
If you are looking to add expenses, this can be done by navigating into a project and clicking on the Expenses link in the left column. Here is a screenshot showing how this works:
When adding an expense there are two fields a field for an expense and a fee. The fee is what is being based onto the client and can include a markup.