Before discussing the Integration, we will discuss the architecture of SharePoint at the architecture level. The diagram represents the architecture of SharePoint and split into two halves. The Left-half is administrator world and the right-half is the end-user world. Everything in right half resides in SharePoint content database. Let's continue with some terminologies before goes into deep dive.
FarmA farm is a logical architecture or logical grouping of SharePoint servers that share common resources of SharePoint. It can be a single machine or more than one machine. The farm is differentiated on their tier levels. Might be possible Farm can be 1to N-tier. Installation can either be done at 1 machine to N. Most of the cases in production you have to choose at least 5-tier architecture for application Server, front-end Server, SQL, AD+DNS, Office Web App Server and Exchange; you can add more than one application server, Front-End etc at any level.
APIs that return all sites in the site collection, a web part called that shows all sites.you need a SharePoint timer service that will run every night to update the sitemap. The time to run the service be configurable.
You can create an Application Page that sits in the ADMIN directory in the SharePoint Root Folder. You need to add a mapped folder in Visual Studio to do this. You can then create a Custom Action which will add a link to your application page, within any area and section within Central Administration that you wish. Here is the tutorial I followed on MSDN for this: http://msdn.microsoft.com/en-us/library/ff798467.aspx Also, the full reference implementation for a timer job with a config page:http://msdn.microsoft.com/en-us/library/ff798362.aspx