I have a PC with 2 drives. A SSD which has my OS installed and a traditional HDD which has all my files and most of my programs on it.
My question is do I have to install my new anti-virus on the OS drive or can if funciton properly on my second drive?

You install the av program while logged into the PC. Where you tell the av program to extract its contents for it to run has no bearing on what the av program is able to do.

it doesn't matter if the av program files are installed on either drive. Those specifics are and other config are generally stored in the registry. The av program will most likely install as a service or during the installation the program will update the part of the registry that loads programs at startup so the OS knows how to start the av engine.

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