I see no reason why they wouldn't work as its only powering the xbee & providing breakout of the pins. The issue I have yet to resolve with this piece is powering multiple sensors on each node, but that's another story.
Have you tried contacting the maker of the Funnel?
I think the main point here is that you are using the XBEE's as a serial line replacement. In this setup I believe they will pair in a point to point network. As a (wired) serial line cannot have multiple clients, I don't think you will be able to get this working in this manner.
Is there a specific reason why you are using the funnel boards instead of the analog inputs on the XBEE itself?
basically once you manage to set up the receiver as controller and both senders as routers tied to the senders PAN ID, they will send to the receiver independently. since you are not synchronizing them, the packets will collide.
this means both senders will send at the same time (chances are the sending will overlap) and the receiver will not be able to process both packets simultaneously and probably drop both. the only solution to this is to send a sync pulse from the receiver with an index for example, forcing the two senders to wait for a free time slot. this will slow you down, especially if you have large data packets or fast sending rates.
and if you add more senders the time-slots will get more and more sparse and the transmission rate slower.
have a look at this paper: Eirik Renton, Collecting Sensor Data for Active Music
Masters Thesis in Microelectronic Systems, UNIVERSITY OF OSLO Department of Informatics, June 2009