It doesn't matter whether you've installed the debs manually or via a package manager, upgrading the package (again either manually or via a package manager) will go fine.

Regarding multiboot: in older kernel-bfs releases you had to create the multiboot entry yourself. If you have done so, then you'll need to remove it manually too.
By the way, not removing the manually created multiboot entry won't even cause any trouble; AFAIK, you'll only end up with kernel-bfs twice in your multiboot list .