Annotation error

We have an application that still requires Acrobat 6.0 used for annotations. We have another application that requires minimun Reader 7.07 for 3D graphics rendering. The problem is, when we upgrade Reader it causes annotations to fail. Acrobat 6.0 is launched through IE 7, which seems to be defaulting to using Reader instead of opening Acrobat 6.0 as we would like. Are there any configuration settings we can use that would "reenable" launching 6.0 and allow annotations to be used with Reader 7?