I am an experienced .NET Developer acting as interim SharePoint Developer, and am new to SharePoint. After determining that I need to go with an application page instead of a site page for a new project due to it's complexity and need of custom code behind. Before developing the entire solution, I wanted to tie up the loose ends of my understanding of application page deployments. I need to add this page as a URL on the left side of a Site Collection page (kind of like what happens when adding a subsite to a site page.) I have read about the modules, which seems extremely hacky to me. There must be a better way to develkop a custom page on top of SharePoint without the page being accessible to anyone on the entire site.
EDIT The application I am wanting to develop on top of SharePoint exists purely for data entry and reporting purposes.