Low Latency PHY in Qsys

Create you own Qsys wrappers for them - if you have the HDL already, all it takes is a TCL file which can in its simplest form be generated by creating a new component graphically in Qsys.

For the higher level stuff, if they don't use standard interfaces (e.g. Avalon-ST, Avalon-MM, etc.) you will need to write wrapper cores (basically HDL that instantiates the other core and converts the interfaces to a standard type which may require some effort depending on the design).