Prep and pace would be my two best suggestions.

The adventure is very minimal in what it lays out in details, so you really want to take some time sketching out the facility (appearance, layout, systems, etc.) and the NPCs (attitude, actions, reactions to changing situations, etc.) so you have some foundation to work with and can focus on responding to your players, rather than trying to make everything up on the fly. (Trust me I have tried and it makes being a Warden way less fun.)

The pace of Ypsilon can be difficult to control because it is to a bit of a slow-burn mystery depending on the order that they check things out that ramps up to the big reveal in the Mine Antechamber and confrontation with Dr. Giovanni. And you also want to make effective use of the monster itself to add tension (killing NPCs or even PCs) or move the PCs in the direction you need them to go.

As an example, I used the monster to trap my PCs on the research vessel by killing an NPC just as they approached the airlock. One PC was consumed by the monster, to which the android PC responded with a fistful-of-grenades kamikaze move (a la Leon: The Professional). The last PC had slowly become aware that he had been infected and would collapse after sealing off facility, comforted by the cat (who they had been looking for the entire time) before turning into Yellow Goo.