Once you've created a Team Project, you unfortunately can't just upload a new process template. As Robaticus says, you'll have to download the XML for the template and modify it, then re-upload it. The power tool lets you create NEW templates for NEW team projects, but it won't modify an existing one.
Instead, you can use the tfsadmin.exe tool (on the app tier under program files\team foudnation server 2010\tools) to export the current workitem definitions and re-import them once you've made your changes.
Luckily, if you're not using workitem tracking much, then this might not be too difficult. You might be able to just delete all the existing workitem types and then re-upload the new types.
If this is too much trouble, consider how much you want to retain your source control history. It might be worth creating a new Team Project with the Agile template and then just moving all your source code into it.