Stacking is not normally allowed in Chess-like games, and I doubt there will be any configurable Chess-variant engines that have this in their repertoire. Probbably the commercial software Zillions of Games could handle it. (But I don't have that, so I cannot be sure. It has the reputation that it can do anything, though, even when it includes cards or dice.)
When no existing program can be configured to do this, it is of course alays possible to modify an existing program. What program you could best take for this depends on the other properties of your variant (e.g. board size).
I created a chess variant based on the Lord of the Rings. It uses an asymmetrical setup, for which I'd like to run computer simulations to test play balance.
There are fairy chess simulators that can do this, except for one problem: I haven't yet found any application that can understand Frodo and Sam, the "stacking bishop" pieces I invented. They move exactly like normal bishops, except that they can pass through, or even share a space with, each other. They begin the game on the same square.
Can anyone show me an app that allows for defining and testing such a piece? I have little coding experience, but if there's an app that allows for entirely new pieces to be inserted into a chess game without too much trouble, I'd love to see it. Thanks in advance for any help.