You should be able to do this without any problems except one. SOPC builder will likely assign the same SLD Node instance to the JTAG debugger in both systems. This will create a conflict when you try to compile the project in Quartus.
I've attached a document that is somewhat old now but you may find it helpful. This was written more specifically for creating multiple instances of the same SOPC system but the principle is the same.
Aside from this issue, you treat the two systems completely independently and shouldn't have any problems. You will of course have to figure out for your self where they get their boot code from.
Jake