I am using Altera parts and package parasitics are s-parameter files (one for transmit and one for receive). They are not part of the AMI algorithmic model.
The package effects might be added into the compiled part of the AMI model, or it might not. The AMI model should include some documentation or sample designs to clarify this.
The readme.txt file says:
** IMPORTANT NOTES **
1) The User Guide, ug375.pdf is located at www.xilinx.com. Navigate to
Documentation and Literature -> Devices tab -> Virtex-6 FPGA Family ->
Virtex-6 FPGA RocketIO Transceiver Signal Integrity Simulation Kit User Guide (PDF)
It provides a reference for these models.