From your description it is difficult to say what your mistake is.
When you look at settings in the MSUB block, do you see the correct target layers?
In ADS layout, do the layers show up at all? You need to add "ads_standard_layers" during technology setup.
Regarding via snap: only layout from schematic elements has "pins" for snapping. If you had drawn shapes on layer "hole" manually, there is no pin and no snapping to other elements. But ADS gives some choices for connectivity check, not sure if there is a setting that can handle this.