How OpenCL handles multiple accelerators on FPGA

1- What do you mean "one PCI-E bus"? For two (or more) accelerators, you need two (or more) PCI-E ports on your motherboard. As long as you have enough ports, you can use multiple accelerators. However, for all accelerators to run at full PCI-E speed, your processor/motherboard chipset must provide enough PCI-E lanes.

2- The OpenCL runtime will see the two (or more) accelerators as separate devices. You will have to initialize the devices separately and create parallel queues for them. Then you can run the same or different kernels on the two board in parallel using one host code. Partial reconfiguration of the boards will likely be sequentialized automatically by Altera's OpenCL runtime.