Well currently to my knowledge there is no support for this. Meaning you're going to have to be clever. I think the only way it would work would be for you to modify the .sopcinfo file. I wouldn't trust myself to do this properly but perhaps you'll figure it out.
Do you really need the systems merged or do you just need them both in the same project. Because you can have multiple and unique SoPC builder instances in a project.
As another note, I have heard tale that an upcoming version of SoPC builder will support "sub-systems". SoPC Builder systems within a system.
Jake