I've decided that just because Maniac Editor can edit the bonus stages, that's no reason for me to not go ahead and make a fork of S3SSEdit anyway, so here it is: ManiaBSEdit! If you're familiar with S3SSEdit, then this is basically the same program. The one change to watch out for is that instead of a simple numeric count of the rings needed for a perfect, you must mark groups of blue/red spheres as having rings by selecting them and clicking the item in the context menu. Marked spheres are indicated by having rings drawn on top of them. Thanks to EyeKey for his RSDKv5 library that this program uses to process Scene files.
Small update, fixes a few things: Fixed Green Spheres not being able to be marked as rings. Fixed spheres that were marked as rings previously not being properly reset when saving. Fixed view resetting when switching windows/changing tools. Fixed crash when starting with grid view off. Slightly improved performance with large layouts.