Hello Emani,
Yes, I believe Target System(Logical system) is maintained in Publication Settings which is used during Forecast Transfer to R/3.
Have you maintained Distribution definition for 51 - Planned independent requirements using SPRO. Note it has to be set up for each location.
SPRO->Integration via APO Core Interface (CIF)->Basic Settings for Data Transfer ->Publication
Yes you are right. Transfer Profile do not tell the system which R/3 system to transfer the forecast. Transfer Profile has details of source of the data in APO (Planning Area/Version/Keyfigure) and Requirement Type in R/3 for PIR.
Additionally, Here is the link which will give you additional details.
http://help.sap.com/saphelp_scm41/helpdata//EN/c9/b4df8870c011d398450000e8a49608/content.htm
Hope this will help.
Thank you
Satish Waghmare