Assuming this is for a FilmFreeway submission, I would make different “projects” for different episodes or festivals. Like, you could have a main one that lists your pilot (make sure to use the link from a playlist so when they click to watch, it auto-plays the next episode in a row), plus one “project” for a particular episode you like (if it’s not your pilot), and maybe one version that’s a supercut of multiple episodes (clarifying that in the description). Slightly more work, but then at least you have your bases covered and don’t get disqualified before people have a chance to engage.
This all said I think sites like FilmFreeway and web fests in general need to have a better way to submit web series because a lot of the time the pilot isn’t the best thing to screen and yet if you take another episode if might be hard to explain what’s going on. Traditional film festivals aren’t build for series, even web fests. That’s got to change because there are some amazing web series out there that deserve recognition.
What’s your web series, btw?