Control Loop Stability of DC-DC Converters
The right amplitude of noise depends on the output voltage. The injected noise should be small enough to not disturb the large signal behaviour of the system. That is to say that it does not interfere with the operation point. 
But on the other hand it should be large enough to be measured/seen. 
typical values are on the order of 100mV but as said is dependent on the output voltage.

You inject the noise across the 5 ohm you inserted in the "broken" loop. so Black on top op the  5 ohm (vout) and red on the bottom.
 This is to isolated the injection points. CH1 measures the output while CH2 measures the input relative to ground. In this way you measure the response of the whole system that is power converter and feedback.