If this is your first DFT project I suggest that you review scripts from past projects. Also visit the tool vendor's help pages, they usually have tutorials for new users. But in general there are other commands you need to provide to setup scan_enable, scan resets, and scan_mode.
For your particular problem, I would start by viewing the netlist and tracing the clock terminal of one of the flops that is violating to see why the top level clock port is not being connected to the flop. You may find that there is a clock mux that is being gated by a top level scan_mode signal that you need to take care of in your insertion script, I.E: set_dft_signal -view existing_dft -type Constant -active_state 1 -port SCAN_MODE
Another issue I have seen with D1 violations is that the clock_gating cell isn't being controlled properly in scan_mode, I.E the test_enable terminal of the clock gate isn't connected properly to the scan_enable pin.
Good Luck