According to audio commentary on the 2000 Anchor Bay DVD, the scene in the motel where the Stuff comes out of the mattress and pillows and attacks the man on the wall and ceiling was shot in a room that could turn upside down, allowing the Stuff to move up and down the wall. It was exactly the same room used in A Nightmare on Elm Street (1984) when Johnny Depp's character Glen is sucked into his bed and his blood is regurgitated back out onto the ceiling.
According to the audio commentary on the 2000 Anchor Bay DVD, some of the substance props or stand-ins for the real Stuff used in the movie included lots of Häagen Däzs ice-cream, yogurt, and, for one scene involving an enormous avalanche-like effect of Stuff crashing though a wall, fire-extinguishing foam. Other shots, such as the ones of the giant lake of Stuff required superimposed images and animation.
According to Larry Cohen himself, in some scenes in which the Stuff chases characters, a foam made of blended fish bones was used. It stank so much that, as soon as the shots were done, the actors ran to a river in order to bathe and get rid of the stench.