How connect 2 FPGA ?

This depends on what speed you want to achieve with your interconnection as well as on the wirelength of the logic interconnect.

It is always good to keep the wires of different IO's the same length to get a uniform delay.

In case you use unidirectional IO you can connect up IO's from two boards. But notice that you will only be able to communicate at about 50MHz for short interconnect wires.

If you do SerDes with accompanying clock for transmission and PPL based synchronization at the receiver side, you can either increase the speed or the wire length.

To get higher speeds on a Cyclone III you can use LVDS differential signalling. In this case you need a 100 Ohm resistor at the differential receiving end. Altera devices also have real LVDS inputs that include a 100 Ohm resistor. So you do not need to add it yourself in this case. You should check the device and the specific differential IO pair. In case of LVDS it is also good to keep your wiring symetrical and the same length and layout it on your board with an impedance of of 100 Ohm.