Hi Nasr,
MAster/slave boundaries are used for 'Periodic structures'. For example,if you need to make a two dimensional array of rectangular cells then instead of doing it manually in HFSS (which is quite hectic)all you have to do is to build a 'nominal(single) rectangular cell' and apply Master/slave boundaries on its side faces(with your desired phase offset between these surfaces) and HFSS will replicate this 'single rectangular cell' into a 2 dimensional infinite array of such cells.The Electric field among successive cells will be matched according to the phase offset 'set' by you while setting up the Master/Slave boundary conditions.
Your second question, PML function and purpose is explained by 'ckshivaram' above. Just think of it like this, In case of an infinitely long transmission line if we send out a signal from one end, we will not get any reflection back as it is infinitely long. So as PML absorbs all of the incident waves with no reflection back it means that on which ever side of your structure you will put it,it will make that side appear infinitely long. Radiation boundaries also serve the same purpose in HFSS.
I do not know what are you trying to do or what do you mean by extending a dielectric box in half space. But if you want to make your structure periodic/infinitely long then you have correctly applied Master/Slave boundaries on the sides of your box and terminating Top side with PML/Radiation boundary will serve the same purpose for top side. Choose 'Incident wave--->plane wave' excitation option and give the appropriate coordinate axes to it according to your requirements and direction and it will work fine.
In the end.Never ignore/neglect the option of HELP in any software you use. Whenever you comeup with a question,try to search it in HELP. HFSS HELP is quite good and you ll find most of the answers from there. IF you are not clear about anything after reading help then feel free to ask. All the definitions written here can be found in HFSS help.
Hope it helps. if you are still unclear, elborate a little bit more what are you trying to achieve in HFSS and i will try to answer you in a better way.
/SC