Are you taking the new puppy and Rusty out to potty before letting them run in the common area? Jmo, furbabies should not have free run if they aren't potty trained.
Sounds like a dominance issue... Rusty is covering new puppy scent. I recommend getting an enzyme/bacterial urine remover (I use Kids-n-Pets or Simple Solution both available at Walmart). Immediately dab up urine and treat area with urine remover (spray where they've pooped too).
Also, if new puppy is being crated for extended periods of time, an x-pen would be a better option (he could have bedding, food and water, potty pad, and toys available to him.
Hope this helps... I only have girls, but it sounds like new puppy needs attention, playtime, and training
