You can, if the two FBO were created in 2 different context.
However, compositing them together on screen in one window will require passing them back to software and then back to hardware in the window's context. This will be slower than just rendering them both in the main context on one thread.
You're better off focusing on getting the rendering into a single thread if it's going to be in one window, and putting your focus on threading elsewhere. Culling and physics are great places to thread (if you have those), but for rendering, one thread per context is the basic rule of thumb (and each window will pretty much mean one context).