Generally you need to :-

  1. import profiles (default, instance, start) into SAP R3
      1.1 add/modify instance parameters such as
            rdisp/max_wp_run, abap/timeout,
            zcsa/system_languages, and so on...

  2. update the R3trans and tp tools with the last ones available on sapnet

  3. configure TMS (systems,layer and routes). 
      You can do it with virtual systems if you have only one SAP system

  4. update SPAM/SAINT

  5. check via Tcde db02 (with refresh option) the available space for TS other 
      than SYSTEM TS.( for the others %used must be less than 90)
      5.1 check to see critical objects (table/index)
      5.2 extend (via sapdba tools -> option TS administration) all TS  which
            shown critical objectsfor example:
            PSAPPOOLD + 200M
            PSAPPOOLI + 100M ...
       You can get necessary via Note 195446 (for language import) and Note 118823 (for client copy)
      5.3 refresh again in db02 and check the %used space

  6. import language other than the default (DE & EN) if necessary

  7. Client copy

  8. configure printer (SPAD)

  9. create user

10. change system user password such as SAP* , DDIC, and so on ...

Error you might encounter at the end of client copy :-

"there is a window "change and transport system not configured" Status is cancelled.

To rectify the errors :-

You need to configure CTS via tcde STMS for your SAP system.

If it's your only sap system, then: 
- configure it as domain controller: run Tcde STMS and accept the default proposed domain 
   controller which is your system
- define one or two virtual system (Menu overview-->system then Menu 
  SAP system-->create-->virtual system)
- Menu Environment --> transport routes then press F5 and Menu Edit 
  Transport layer to create a "Z" layer for example "ZDEV"
  Create a transport route between your real sap system and the virtual system 
  by using the two layers: "Z" layer and "SAP" standard layer
- save and distribute the TMS configuration

That is the main action you have to do to setup CTS.
 

Best regards,
SAP Basis, ABAP Programming and Other IMG Stuff
http://www.sap-img.com