"the little box where the tire jack is kept? is there anything sitting under that that i would need to move or be aware of? i was wondering if i could cut that bottom out and make it bigger to hold more stuff?"

It's the cross air duct for the rear HVAC.

When I removed my 3rd row seat and built the ''false floor'' in the back, I considered removing the OEM jack storage. I decided to leave it alone because of the duct work.