Your big dog should be trained not to be possessive of toys or chews.
Swissys have various degrees of herding instinct, some with very strong drive and others with moderate drive. Strong herding drive pairs closely with strong prey drive, leading to a desire to chase small animals. Swissys should be taught from an early age to not chase small animals such as cats, squirrels and small dogs. Strong herding drive can also lead to games of chase and tackle with small children if not directed and trained properly. GSMDCA.ORG
How big is your yorkie and how old? I think I'd be afraid to ever leave a tiny yorkie alone with a dog that size that has already shown that he would willingly hurt the yorkie.