Once there would be an Advanced button allowing us to define a template path for each search-box, it'll be much easier for sure.
Right now, I embed my custom searchboxes in widget templates (i.e. blog list template) and it works. But this is not the ideal solution, just a workaround.
If someone out there need this workaround until this bug is fixed on a stable release...
Simply add following in your widget template:
And don't forget to include:
<%@ Register Assembly="Telerik.Sitefinity.Search.Impl" Namespace="Telerik.Sitefinity.Services.Search.Web.UI.Public" TagPrefix="sfSearch" %>