To check whether you're using IMAP or POP3:
Long press the account, then Account setup -> Manual
Now you should be looking at the Incoming server setup page. The account type (IMAP or POP3) is listed right at the top of that screen (just below the title bar).
To reconfigure as IMAP (if it's POP3 now): Menu -> Add account in the account list "window", then just enter yoru name / email / password and press Next. The app has a preset for @yahoo and it's IMAP. Once that's done and you're happy with how it works, you can delete the old account from AquaMail by long pressing it and choosing "Delete account".