As far as I know, Gmail (as a mail service) is somewhat special in how it deals with the deleted messages. So, the proper way of deleting messages for Gmail accounts is to move the message to the server's Trash .
Aquamail has a built-in "[Deleted]" folder. It can be "mapped" (and synchronized) to a particular folder on the server (in many cases called "Trash"), or it can be left not configured to sync to any folder.
When you set up a Gmail account in Aquamail, Aquamail is smart to recognize Gmail, and maps (with syncing) "[Deleted]" to Gmail server's "Trash".
When you set up a non-Gmail account in Aquamail (connecting via IMAP), Aquamail may or may not guess properly (or at all) where to map [Deleted].
I suspect in your case, with what you call "IMAP account", [Deleted] is either not mapped at all or mapped incorrectly. So, it doesn't sync with the correct folder on the server.
You can check where [Deleted] is mapped by a long-press on the left-hand-side of [Deleted] in the expanded account view. (It will have a colored left top corner if it is mapped/being synced, I believe.)
To choose the folder to which you want to map your [Deleted]
[long press on the account in the account view] ->Options and Folders -> Folders