Most of Kotomine's Command Spells are actually inherited by his father and the previous supervisors of the Holy Grail Wars at the end of the war, since a Master can only obtain 3 from the Holy Grail.
In addition to his own Command Seals on his lower left arm, he also has Command Seals inherited from his father that cover his right arm from the elbow to the wrist. The supervisor of the Holy Grail War is entrusted with the Command Seals recollected from previous Holy Grail Wars, so he has access to a great number of them.
He of course got all of the Command Spells that Risei Kotomine had after Kayneth Archibald El-Melloi killed him. And because his Magic Circuit is still underdeveloped by the time of the Forth Holy Grail War, he uses Command Seals as makeshift Magic Circuits and sacrifices them, similar to how Shirou sacrifices the Magic Circuits he made during his training when he does Projections (as noted when he projects Excalibur).
The Origin Bullets utilizes Kiritsugu's Origin of "Severing and Binding"
The "Severing" aspect will cause prana stored within the Circuits to ignore the paths within the body, flowing chaotically and destroying it in the process. Afterward, the circuits will be bound together again with the "Binding" aspect, albeit in a chaotic and useless manner, thus rendering them permanently inoperable and destroying the target's magecraft abilities.
However, since Kotomine is using Command Spells as Magic Circuits, the Origin Bullets affects the Command Spell Kotomine used and leaving the others intact. Kotomine doesn't fight like an orthodox magus which Kiritsugu has fought in the past, and the fact he was even born with with Magic Circuits is abnormal by itself, so Kotomine isn't your typical Magus.
As for what Kotomine knew of Kiritsugu's abilities, while he probably didn't know them at the time he was still a skilled Executor, it's noted that he's skilled enough to judge the type of bullet by the sound of gunfire and able to analyze the situation calmly. Coupled with his own physical prowess and how he uses the Command Seals to reinforce his own body and equipment, he probably figured out Kiritsugu's bullets weren't normal and prepared a suitable Anti-Magus Defense (devised from experience hunting strange Magi in the past for the Church) backed by Command Spells as replacement for a Magic Circuit. And as we can see, he quickly worked out how to defend against Kiritsugu's bullets.
