To repeat myself:

• Kobo desktop for Kobo bought books
• ADE for library books and other DRM books
• Windows Explorer (actually OSX Finder) for Mobileread and other epubs or PDF/TXT/RTF docs

I don't actually read epubs on my computer so this works fine for me. Should I get an iPad this will need to change.

It's not that Calibre itself is "bad" but rather that the Kobo file management plugin seems to be still flaky after many months of opportunity to make it not so.