What is a puss filled sac on the side of my toe? When I popped it and cleaned it out there was yellow liquid, and a black whole between skin & nail.

Paronychia nail pus. Infections and abscesses near nail plates are common, especially after improper manicures. The red pussy painful bump may need to be sterilly drained by your dermatologist. Then antibiotics may be needed, both topically and orally.
A Nail Tale. This sounds like a paronychial abscess which you just drained. An infection in the skin margin made with your nail caused the pus (white blood cell warriors) to collect under pressure. When you released the pressure the pus drained and the yellowish fluid (serum) is a filtrate of your blood and tissue lymph (another fluid). The resulting black hole is the cavity which will close with healing.