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The vector table is not placed inside the PCIe IP (hard or soft). Instead, the application has to present it behind the application interface (probably Avalon ST), and the values you enter in the MegaWizard for the address offsets and BARs denote your application’s expectations of those accesses.
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Yes. I'm get one megabyte in PCI memory and set MSI table to 0x80000. I'm make four 32bit registers for data and address ({32_bit_adress_low,32_bit_data}). But this is only low 32 bit of address. MSI-X required full 64 bit address. For generate IRQ I need generate memory write with 64bit address {32_bit_adress_high,32_bit_adress_low} with data in "32_bit_data".