Thank you Colm! That solves the issue, specifically this page 
http://http://help.sap.com/saphelp_nw70/helpdata/en/46/95ad62e85613eae10000000a155369/content.htm
1. Specify the target source systems
If you also want to collect source system-dependent objects, choose Source System Assignment to specify the source systems for which you want to collect objects. Only those objects that are assigned to the selected source systems are collected. If you want to collect source system-dependent objects but have not selected a source system, the dialog box for assigning source systems is displayed automatically.
I remember seeing a "specify source system" pop-up when I first attached my PC_FILE sourcesystem transformation to a transport. I now realized I chose the wrong source system, because there was no PC_FILE in the choices. Only the ECC source system was available.
Which means after BASIS team creates the PC_FILE source system, I will have to assign my Transformation to the PC_FILE source system and Transport it again to target system.
Also, If your BASIS doesn't know how to maintain the PC_FILE mapping in the RSLOGSYSMAP table, this can be done via Transaction RSLGMP.