Yes; you can totally accomplish what you wish without a deep knowledge of TFS. I will provide some tips that I hope will save you a lot of time without looking through all the MS documentation and you might even consider a different route after you read this...
First, know that there is a customizable set of files that comprise a Process Template; a Process Template is the template and instructions used to create a new Team Project, so you are likely familiar with it already if you have set up a working TFS Server before. The Process Template consists of a directory structure of XML files and artifacts such are reports and SharePoint portal site content. There are 2 Process Templates that come out of the box with TFS 2010 (MSF Agile 5.0 and MSF CMMI 5.0), and people create their own all the time. You can find example of custom Process Templates on CodePlex.com and throughout the web; they will contain examples of custom SharePoint site templates that will get deployed when a new Team Project is created.
So one way you can accomplish your customization task is to start with an existing Process Template like the MSF Agile 5.0 that comes with TFS 2010 and modify the SharePoint content to suit your needs. You can find specific, detailed pointers on how to do this using the following MSDN guidance: http://msdn.microsoft.com/en-us/library/ff678492.aspx. To get started, check out the process template yourself by downloading it to your computer (http://msdn.microsoft.com/en-us/library/ms181511) and then navigate down through the folder named Windows SharePoint Services to find the portal content. If you replace the SharePoint content there and then upload the template back up to your server, new Team Projects created with it will have the modified SharePoint site.
Another option is to create new Team Projects without a SharePont site (as this is now option in TFS 2010 and moving forward), and create a new SharePoint site separately based on a modified version of the SharePoint template you made, and then connect the Team Project to the site after the fact through the Team Project's settings in Visual Studio.
If this customization activity is something you are doing within your company, please know that you don't need to create a new Team Project each time you have a new software application you are building or even for each team in your organization; it's a broader topic, but most of the time I find that creating new team projects all the time is overkill one can consolidate all development activity into a set number of team projects and split them up using Areas and Iterations. If your teams can utilize existing team projects then it really reduces your costs for maintaining all that is created when making new team projects like folders in Reporting Services (SSRS), SharePoint sites and all the security management and configuration that can go with implenting a new Team Project. If you consolidate, you can still split up the reports and sharepoint sites by using different folders in SSRS and pages or documents liraries or even sub-sites in SharePoint. There are good reasons to have separate team projects, but I find that most of the time companies only need a handful... think about it and let me know if I need to clarify, as it can really make your life easier.