Using the "Register COM dll" checkbox uses regsvr32, which calls DllRegisterServer in your dll. This works on both x86 and x64 systems, however only on "native" dlls. That is, you have to use RegAsm for .NET dlls.
We plan on integrating RegAsm support within wyBuild in the near future, but in the meantime you have to execute a simple batch file that uses RegAsm.
Does this help?