You need to decide where you need the integration touuch points between these systems. So, you need identify the business processes where the integration is happening.
A quick example in CRM - R/3 case could be Quotation to Sales order.
CRM has the in-built Middleware which performs the integration between CRM and R/3 system.You can transfer the custom data either from CRM to R/3 or vice versa. Initially, you need to verify the RFC Connections between the connecting systems. Next, you can do the initial download of Customizing object,Business Objects and Condition Objects from R/3 to CRm.
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