master pages in 2010

Question

I have a question about understanding how the master pages in C# 2010 web application are linked (wired together). I am asking that question since I believe I and/or my co-worker placed some test code in the location where the production code was actually stored. 
  What is happening is when I try to debug the  production application using iis 7, a reference to a master page and/or an *ascx file   is lost. The file that it is trying to access, is for a test version of one of the production modules. This test version of the production code is mainly commented out in the code right now. The part of the test code that actually is running is the startup file name that looks like 'startup2.aspx'. The test code is actually calling 'startup2.aspx' instead of 'startup.aspx'. 
   Thus to understand how the master pages are wired together I am thinking that I will debug the application from the time any code starts running. Can you tell me if this is a good idea?
   Also I am wondering if you can tell me how master pages are actually 'wired' together? is there a good reference that I can look at?