The thing is, if you're trying to integrate the application or page into DNN you basically need to make it into a module. I'm going through the same stuff myself. The process to do it, is kind of straight forward but does get you into many issues depending on what you're trying to do. For me I'm actually replacing an existing auth system so I'm going through hell. This is the basic steps you can follow to get started.
Start opening your installed DNN Solution with VS
Add your project to the DNN Solution
Open the BuildSupport Project in DNN and add a reference to your project
rt-clck the solution and open the configuration manager and uncheck all of the projects except buildsupport and yours
Add your aspx, aspx.cs and aspx.cs.resx files to your projecct (assuming you're using C#)
Then rename your aspx file to ascx (the others will change automatically)
Now, for the main changes.....
Open the ascx file and only keep what is in between your <form> and </form> lines. Just delete everything else.
Recreate your code line with:
<%@ Control language="c#" Codebehind="AllBundleList.ascx.cs" AutoEventWireup="false" Inherits="TangentApps.MessageManager.bundle.AllBundleList" %><%@ Control language="c#" Codebehind="pagename.ascx.cs" AutoEventWireup="false" Inherits="fullclassname" %>
where pagename is the name of the code behind page and the full class name is yours. My line looks like this
<%@ Control language="c#" Codebehind="AllBundleList.ascx.cs" AutoEventWireup="false" Inherits="TangentApps.MessageManager.bundle.AllBundleList" %>
Now open the ascx.cs file and put in your code. Add the DNN things like
using
DotNetNuke;
using DotNetNuke.Common;
using DotNetNuke.Common.Utilities;
using DotNetNuke.Entities;
using DotNetNuke.Entities.Users;
using DotNetNuke.Entities.Modules;
using DotNetNuke.Services.Localization;
using DotNetNuke.Services.Exceptions;
and your public class line to have
: DotNetNuke.Entities.Modules.PortalModuleBase
There are other things to be done based on what you've got but that will get you pretty far. You can also go to DNN Jungle and install their templates for VS. Extremely helpful site because they also have walk throughs for integrating.
Once you've got it there at it builds with no errors then login to your DNN go to the Modules page and add your module and control to the list. Use one of the existing ones as an example for how it should look. Hope this helps. If not spend lots of time on the DNNjungle site. http://dnnjungle.vmasanas.net/