1080p mode will guy you a slightly wider field of view where the 3mp mode will chop off the edges to keep the image a little more square-like. Never tested the CPU, but I would imagine the 3mp would use a bit more...The best mode to run it in will depend on what you're using it for and what level of resources are available.
If you're using it simply to monitor your yard, 1080p is all you need....If you happen to need the slightly wider field of view, the 1080p is what you'd have to use. Also, if your computer resources or network bandwidth is limited, 1080p may be best....
On the other hand, if your resources and bandwidth support 3mp and you don't need the extra bit of width, then 3mp is going to provide more detail. This is especially recommended if you're trying to identify a suspect, read a license plate or if you're using the digital zoom feature.