Ah, neither of those programs are specifically supported. I haven't even heard of shakespeer before this.
As for Transmission, it doesn't really have a way of marking the files themselves as incomplete. Instead it has the ability to use separate folders such that when the download is complete, it will move it to a special folder for complete downloads. If you do this and want to purge files out of your folder of incomplete downloads, you can have Hazel monitor that folder and set up a rule to trash files after some amount of time. You can base it on date added or date modified, depending on your needs.
Let me know if you need any more clarification on this.