yes, you can simulate your layout structure in the EM Sight (this is part of MWO, its availability depends on your license options). You can import your layout as gdsii or dxf files.
MWO has a 2.5D EM solver meaning that can only simulate planar multilayer structures and not arbitrary 3D...
If you have multilayered planar geometry (with vias), then you can simulate with MWO. If you have complex 3D geometries then you must switch to either Microwave Studio, HFSS, IE3D, Feko or any other full wave 3D solver...
You can import dxf to MWO, the problems you might encoutered is that you have to snap the structure to a fix x-y grid to have accurate results. If you have some fine details in your geometry, they might be lost or simulated incorrectly if you don't snap it. Finally, if you make your grid very fine to represent accurately your structure, you might end up with large matrix size (memory requirement) and increase the simulation time drastically. However, this will happen to some degree in other suggested simulators as well.
The schematic is simulated in the the linear simulator. The layout is simulated in the EM simulator. To simulate a schematic in the EM simulator, you have to generate the artwork from the schematic first. After a quick check with the schematic, I usually draw the geometry in the EM simulator and leave the schematic behind since a lot of my structures are not schematic elements. Its almost as fast to draw the geometry as it is to draw a schematic.
The schematic is simulated in the the linear simulator. The layout is simulated in the EM simulator. To simulate a schematic in the EM simulator, you have to generate the artwork from the schematic first. After a quick check with the schematic, I usually draw the geometry in the EM simulator and leave the schematic behind since a lot of my structures are not schematic elements. Its almost as fast to draw the geometry as it is to draw a schematic.
You can simulate a via and chipcap in a schematic wih the linear simulator. But I think you get better results using the EM simulator. The EM simulator can do vias but you may have to create your own model for the capacitor.