In one system copy, after db restoration directly went to t-code STMS and gave "Transport control domain" for the target system.they didn't do any changes in SE06-->CTS config.
I have refered another document in that they have done(mentioned)
1. Select the Database Copy or migration option
2. Press the Post-installation Processing button.
3. When prompted Do you want to re-install the CTS?, press the Yes button
4. When prompted *for* the Source System of Database Copy?, make sure that the of the production system is selected. Press the checkmark button to continue.
5. When prompted Change originals from PRD to QUA?, press the Yes button
6. When prompted Delete TMS Configuration?, press the Yes button
7. When prompted Delete old TMS configuration?, press the Yes button
8. When prompted Delete Old Versions of transport routes?, press the No button
Let me know what is the difference and where we do CTS config.Both are system copy from Production system