I put my case temp sensor around the chipset heatsink on the mother board where there isnt a lot of air flow that way i get what i feel is a temp that displays something more accurate than if i put it where there is constant air flow. as for the intake, i would again put it in a low air flow area so you can get more air moving through your case.....just my opinions though not scripture
I use software to monitor my cpu and chipset temperatures. My antec p160 has 2 sensors. One is taped onto a memory stick, the other is attached to one of my 4 hard drives.
Depending on your system, use Speedfan. It is a nice little util that will grab all the sensors (including HD if it supports). and show you current temps..