Orange spots are very likely Cedar Apple Rust. Not much you can do with fungus once the tree is already affected. Fungicides are preventative so you have to start spraying before the CAR spores are released in the Spring(about bloom time) and keep spraying near weekly until it gets to hot to produce the spores ( about this time of year here, when temps start going over 80F) But to get total control you would need to spray through September. You can monitor a known gall on a cedar tree though to get exact timing. In order to prevent CAR, you have to really love your apples, I just let my susceptible trees get it unless its a yard tree that Im going to be eating. Planting resistant trees is the only way to really get away from it without spraying alot. THere are several fungicides that can be used, Immunox is probably most popular.