Hi Dan,
This is a current limitation of the designer. This is why the addin creates a partial class with two files (MyFile.eto.cs and MyFile.cs). The *.eto.cs (designer) can only contain generic Eto.Forms UI, whereas anything you need from your project should go into MyFile.cs. This does make it difficult to use custom controls in your UI, but you can create a Panel as a placeholder then set its Content to your custom control in the MyFile.cs partial after the panel is initialized.
I haven't been able to figure out how to add references to your project from VS 2015. Ideally, it'd be great to hook into the vshost.exe that is usually created for your project, but again I have no idea how to do that and couldn't find anything online. Perhaps this could be done by referencing the files from the output directory, though if you have copylocal=false on any other references that might still make things break.
Another issue that I need to figure out is to use a separate AppDomain to do the compile/load of the preview when using code-based preview (xaml/json doesn't currently have this issue). Each compile currently adds memory overhead to VS, which is not too bad right now, but adding your project references will make that bloat very fast. I have the designer working using an AppDomain in standalone mode, but it just doesn't seem to work when hosted in VS..
Any help on these would be certainly appreciated! The VS addin infrastructure is not really all that straightforward and it feels like I'm flailing about when I have to try 10-15 different ways before getting something to actually work.
Cheers!
Curtis.