If you want to use Codebehind and compile the C# into a dll then you should create a new "Web Application Project" in your solution. Set project references from this project to any of the mojoPortal projects you may need like mojoPortal.Business, mojoPortal.Web, etc.

Then use post build events to copy your .ascx file(s) up to the Web/yourcustomfolder and copy the dll to the Web/bin folder

You can see example post build events in mojoPortal.Features.UI or in WebStore.UI, right click the project and go to properties.

If you want to use controls from mojoPortal.Web in your project you need to declare them in the Web.config file of your custom project in the <pages><controls section

You can see examples again in the projects mentioned.

Hope it helps,

Joe

You will need references to mojoPortal.Web and other projects, mojoPortal.Business, mojoPortal.Business.WebHelpers

You should not change the SearchResults.aspx.cs in mojoPortal, if you change things in mojoPortal you will not be able to get upgrades without losing your changes.

You could create a new SearchResults page in your own project and then use post build to copy it up to Web folder replacing the one there. That way your custom code is always in your own projects so you will never lose it. Use your own namespace and class names in your custom version. First copy the code from mojoPortal existing version and get it working from your project using your post build event to replace the existing one in Web. Then you can start customising your version. Whenever you make a change whether in your .aspx file or in your .aspx.cs file you have to build again so the post build will copy the files again up to Web so you can see your changes.

If you have any trouble about the master page reference just create an App_MasterPages fodler in your project then add a new master page there named layout.Master

Hope it helps,

Joe

You are of course free to do as you wish.

If you are developing against the pre-compiled release, then you will be able to upgrade because you are not modifying any of the C# source code because it is pre-compiled in the dlls. But still if you modify the .aspx or .ascx files you can lose your customization if you upgrade, or your custom copy may no longer work if the original version has changed internally.

I generally recommend developers to work with source code. The biggest benefit is there are examples of code to do almost anything you would typically want to do. If you want to do anything that is similar to any existing functionality you can review the code and learn how to do it. And you can find lots of little undocumented helper methods that make things easier.

Its always possible that bugs will be found and you will want t be able to upgrade to get bug fixes.

Also mojoPortal is constantly improving and getting new features and functionality. I think its a bad assumption that you will never need or want to upgrade. Never is a long time. 

Hope it helps,

Joe