Hi Suparna and Raghuraman,
I believe that there is a way, which I could find a long time back but now remember to only some extent.
If you make the QOS as EOIO in Processing tab, on the same page there will be some option below to choose the queue name. In this manner you can prioritize the queue for a particular interface. You can may be specify the name for example as XBTRQ*. So all messages of that interface will be in queues like XBTRQ001, XBTRQ002 etc.
I hope you are familiar with the queues management. That is, in ECC in t-code SXMB_ADM, in Manage Queues, you can manage the queues. However, before this you can register the queues of ECC system/SAP Non-PI system via t-code SMQR.
@Both : This is just an attempt to sort out the issue 
Regards,
Souvik