Yes it is possible to mix different Cyclones in this configuration. Have a look at page 7-9 of this document (http://www.altera.com/literature/hb/cyc3/cyc3_ciii51008.pdf) to see how to connect several Cyclone III in multidrop mode (called BLVDS by Altera).
I would suggest that you define all your inputs/outputs in two Quartus projects for both FPGAs, assign pins and do an I/O check before you route your board, just to be sure that your choice of pins and I/O standard is possible. When routing the board, pay special attention to the LVDS pair because any brutal change of impedance on the line will cause reflexions and degrade the signal. You must have stubs as short as possible between the LVDS pair and the FPGAs.