There are differents ports in HFSS wave port , lumped ports. See the Help for more explanation. Wave port are used for wave guide structure (coax, hollow wave guide), when the transverse geometry is constant along one axis. Lumped port are used to feed antenna or other microwave system like coupler, filter ...
Bondaries conditions depend on your structure.If the system is closed bondaries depend : it must be a perfect E conductor if there are no loss, perfect H , it must be lossy (complex permittivity , complex permeability, finished conductivity).
For HFSS to defined a problem you have to construct the geometry of your system, define the bondaries (the material and the excitations). In fact it is just the parameters of the Maxwell equations solved with the finite elements method.
Bye for now.