I was on set for this episode in the audience (really cool experience) so I can answer how they did the alligator as well as any other questions I feel comfortable answering from being there. They filmed just the alligator the day before the live taping without any cast members. Than the day of filming they filmed just the cast (Matt and DJ) without the alligator actually there and digitally inserted it together in post production.
Also the scene that mentioned Ramona having to eat in the Janitors closet was actually filmed but cut from the final product of the episode. It was filmed right before Jackson slips on the Bologna but was apparently cut from the episode. Also the final scene and the second to last scene were filmed in reverse order and Tommy did something cute with the blocks (I don't remember what) in that final scene that got cut. Otherwise what was filmed and the finished product were pretty much the same from what i remember.
Now as much as I enjoy this show (and I liked the previous 2 seasons better although this one had its good moments) the moment I stepped on set this summer I could of predicted everything that happened from here on out this season (Jackson and Rocki with Lola departing, DJ with Steve, Stephanie's baby etc.) save for Kimmy being the surrogate mom which surprised me.
If anyone else has other questions about this episode or the set I will try to answer it if I feel comfortable or know the answer. I met some of the new cast very briefly and they were super nice (I am not going to disclose who) but none from the original show after.
Her name was Siena in the show (they never said her character name but they introduced her in the curtain call after which revealed it).
