How to connect on-chip FIFO in QSYS?

Are you sure you are enabling the RCON and WCON bits in the control register of the DMA? With the memory mapped FIFO you need the DMA to access the same address to read/write to the FIFO and by default the DMA will increment it's access (for memory to memory type operations).

So to read data from the FIFO and shoot it across PCIe you want to have the RCON bit set to 1 and WCON set to 0 (read from fixed address, write to a block of memory). To write data over PCIe into the FIFO you want to set RCON to 0 and WCON to 1 (write block of memory to fixed address).