Ideally CLP checks are run at three stages to the minimum - RTL, Logical Netlist with LP structures and Physical Netlist level (power, ground connectivity)
At RTL level - to ensure that the CPF written is correct and all required definitions, rules are added. Logical is where you do strutural checks on ensuring that the LP structures are added as per rules and sitting in the correct domain and all required signals are isolated. Physical level is more abt power connectivity checks ensuring that the required power domain gets the correct power supply etc.
Not sure what tool your using to insert Isolation cells, but if your using RTL Compiler, from there you can directly export a dofile to execute CLP - write_do_clp