Definitely the last method you tried would be your best bet. However, instead of creating each feather as a separate subtool, you should create them all in the same subtool and make use of polygroups and mask by polygroup. That way you won’t have dozens of subtools to contend with.
So you can mask off and ctrl+drag the transpose line to duplicate each feather. This will, in turn, automatically mask everything else off and allow you place each feather as you create it.
Or alternatively, you could create several feather model variations, save them as insert mesh brushes and do it that way instead.