I just built my first computer and i plugged the 4 pin floppy connector that comes out of the power supply into the system fan spot and it was for the floppy drive. but i dont have a floppy drive but the wire coming from the power supply was supposed to go to the floppy drive but for some reason i plugged it into the system fan spot and i was woundering if doing that would short out the motherboard and cpu? the computer comes on but then shuts off after like 1min and nothing comes up on the monitor.

Welcome to TS
If I got this right:
You plugging a 4 pin mini molex (used to power a floppy)into a three pin/post system fan port on the motherboard?
"some reason i plugged it into the system fan spot"
Have you seen a bright light and blue smoke yet?
Un-plug it see what happens...

G'Luck