Oh, I've just re-read SRyLul's question and realized I didn't really answer his questions. :-[ Let me try again...
The home skype is setup to auto-answer ANY call from skype users in its contact list, so you should setup a dedicated skype user just for the skype home machine. You then add "real" skype users as contacts that are allowed to call to skype home. Only those people can connect to the home skype, control the SkyDuino Widows app, and the Arduino.
I don't know if Skype require a server or if it would work in closed network or not. Sorry.