I have an aspx page that get copied in the layouts directory of a Project Server instalation. The aspx is a web part page that has a web part zone. How can I add a web part in the markup of the page, within the web part zone?
You cannot have customizable Web Part pages in the layouts directory! This is only supported on Web Part pages stored in a document library or other folder in an SPWeb, i.e. ASPX files that you can get an SPFile reference to. Web Parts on ASPX pages in the layouts directory must be added as Web controls in the ASPX source.