I am building my first pc and I have the Cougar Challenger case but I dont know how to put the motherboard in.

well, what motherboard do you have?

The orientation of the motherboard should be self-evident from where the I/O ports on the back of the motherboard are - they have to match up with the cut-out on the case.

In addition, you screw stand-offs into the backplate in the case to match up with the screw holes in the motherboard (should be clearly marked and also in the documentation) and then you screw the
motherboard to the stand-offs.

Did you buy a motherboard form factor that is supported by the case? ATX, micro-ATX and mini-ITX are common form factors for motherboards. SOme cases support all, some not.