The standard way to do this would be to have one solution file and add both those projects (Kentico website and other class project) to your solution. Then add a reference to that other class project in your Kentico website and it will automatically build that class project and copy the dll to your Kentico site.

If you support DLL requires Kentico DLL's then you need to have those referenced in your support DLL so it can build them and distribute them in your support DLL as needed. Sounds like you might be donig too much of once thing and not of another. To make things simple, you should keep your support DLL generic and simply pass objects, properties, values back and fourth. OR simply leave your custom code in your website (I'd recommend this option).

I have a few ways about this:

1) for client custom code, I use the best practice from Kentico and add a directory in the /App_Code directory with the same name as the site code name (in CMS SiteManager>Sites>Code name).

2) for my custom code that I use in many of my projects I create a directory called /App_Code/KehrenDev/ and add any classes I have there that may not be specific to the client or site but simply generic functions or methods that I find helpful and Kentico doesn't offer. By Default, this directory will not be part of any export if a client exports their site.

Best of luck
Brenden

Figured this out, though I still am unsure if things are all good...

I thought maybe this was related to the application of hotfixes to the Kentico installation and it seems to be. Essentially I downloaded hotfix 56 and extracted it separately and changed my library to reference the DLLs in the hotfix directory instead of the web project's /bin directory. This worked just fine and my site loaded without any issues.

The mystery to me is why the website worked with the existing DLLs in the /bin directory, are all the DLLs from hotfixes in the GAC?