HI,
Follow this wonderful document to setup connections between two systems.
http://scn.sap.com/docs/DOC-11738
You need to ensure all your landscapes are interconnected well. You need to ensure always your WAN connected. RFC between your R/3 and BW should be monitored by your BASIS team regularly.
Two imp things in simple terms: First your WAN should be Ok and then your RFCs.
Regards,
Suman