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.
Have you considered using a Webpart?
With a visual webpart which is essencially a usercontrol wrapped in a webpart you can add as much complexity as you want and you also have code behind to hook to events etc.
The benefit of using a webpart is that you can then drop it on a page, and use all OOB sharepoint access controls.
You mention that you want to develop a data entry reporting app. So something you can do is to create a subsite. Look all access to modify pages except to owners. Create all your screens by adding pages to the subsite and dropping webparts on it with the logic you require for each screen.
Also make sure you deploy the werbparts via a web feature that only is activated in your subsite, this way the webparts are only available in that particular subsite.