There is a change from 2000 here, and it's not documented in Book Online yet. To further confuse matters, in some earlier builds of Yukon\Whidbey you'll actually find multiple copies of RSReportDesigner.Config on your disk, so you can't always key on it's location.
On the report server, copy the file to the \Reporting Services\ReportServer\bin folder, just like you always have. You still use \Reporting Services\ReportManager\Bin, too.
On the client where you design your report, the best idea is to search for Microsoft.ReportingServices.Designer.dll. You'll probably land in C:\Program Files\Microsoft Visual Studio 8\Common7\IDE\PrivateAssemblies. Your custom assembly and RSReportDesigner.Config file should live with the designer assembly, and you can ignore other instances of RSReportDesigner.Config you might find elsewhere (like in C:\Program Files\Microsoft SQL Server\90\Tools\Binn\VSShell\Common7\IDE)