Just wondering how I would go about this. If I go to convert an album an extra stuff in the folder like cover art, logs, cues, isnt passed on.

It seems a hassle to have to manually copy and paste album art from every folder, surely there is a quicker way of doing so?

Unfortunately, it cannot be done automatically right now.

When outputfolder is the same folder as sourcefiles you could use Move to after conversion to move all folderitems, including cue's and other stuff.

or use dbpoweramp to do everything you want to do in one step.