That is a good question
Firstly, some sites e.g,liver, lungs, bone,brain lymph glands are the sites of choice for secondaries..........not always, but mostly.
Secondly.......Secondaries have typical X-Ray appearamces......mostly but not always.
Thirdly and the most importantly.... biopsy.To biopsy and see malignant tissue which is from an organ in a distant part of the body i.e colon tissue biopsied from the liver would indicate a secondary.
The pattern and picture of the biopsy is crucial.
It is not uncommon in medicine for the secondary to appear first and then the hunt is on to find the primary and it is not unusual for the patient to die of malignant secondary disease without the primary ever being found.
Bone secondaries like your friends commonly have the primary in breast, or lungs or colon or thyroid and that are the first places to look.