A tip that might help: For audio and subtitles, try using Track Selection settings instead of Track List settings, and once you have all your choices selected, save them as a preset. Then when queuing episodes, choose that preset.
Also, consider doing a test run on part of a single episode before queuing up a batch. (Choose a time range of just a minute, for example.) That way you can check the result quickly, and adjust if necessary, before committing to the whole job.
Finally, I recommend using Add To Queue for each episode, then Start once they're all queued.