Yes, you COULD use colloidal silver in a Neti Pot, but you would use an awful lot of silver rather wastefully. I have several refillable nasal spray bottles I fill with colloidal silver solution. You could use the Neti Pot with buffer solution to clean out your sinuses first, then nasal spray with silver while snorting it up. That should give plenty of silver into the sinus cavity. Also you can spray some into your mouth and throat while inhaling.
For deep lung issues, get a small ‘travel nebulizer’ and put a teaspoon of colloidal silver in it to deep inhale the mist.