Mobo defective, where should I put my CPU while waiting for new mobo?

You'll have to clean the old paste and apply new one, before reinstalling it, so you can do it now.
I would put it in its box (if still available or similar). Take care to not bend the pins.
Depending on the motherboard, you might need to update the BIOS for the FX to work.

Put the CPU in the plastic box that came with it. And as far as i know you need to replace the thermal paste every time you remove the heatsink.

+1^^
You will want to clean the off TIM from the CPU's heat spreader and the cooler too. If you don't want to get a commercial cleaner like: http://www.amazon.com/gp/product/B002DILLMS/ref=s9_simh...
...you can use isoprophyl alcohol instead.
However, something like the above will include the new TIM to apply to the CPU before installing the heat sync.

Instructions...
Cleaner: http://www.arcticsilver.com/pdf/appinstruct/ac/ins_arct...
TIM: http://www.arcticsilver.com/amd_application_method.html...

Thanks for the help everyone. I bought Arctic Silver thermal paste and thermal paste remover for my CPU and also the Mobo is an Asus 990X EVO R2.0 so the FX works out of the box.

Right now it is in a plastic ziploc bag with the pins facing up and I pressed the inside and outside of the bag to a grounded surface (my fridge) to remove any static it may have had. The bag with the CPU is inside a closed cardboard box so I think my CPU should be fine. Either way, its still in warranty so I guess even if it doesn't work I can just get it replaced.