Having 2 lists on the Episodes page was a feature requested for a long time now. Some users even reported they're using 2 accounts on Next Episode to be able to keep track of their Acquired and Watched episodes.
For Premium members, in the Episodes tracking page, there is now a "Show Acquired Status" toggle which adds an acquired status checkbox to all episodes. Clicking the checkbox (or the season episode number of the show) will mark it as Acquired, and clicking on the [-] will mark it watched as before.
Check it out and let me know how it works for you and if you're happy with the implementation!
Update: Added filter to switch between All Episodes, Not Acquired and Only Acquired!