With the stock o2 sensor plugged in, the ecu uses it (closed loop) for cells in the AF table with values of 14.57 in the old stock exhaust tune below 15% throttle and below 4200 rpm, so it's more than just idle. It doesn't output an a/f ratio, just a +/- to indicate if it's fat or lean.
There's really no reason to use the stock o2 except for emissions so don't bother. The plug you put in is probably the same as the plug used with the power commander. It tells the ecu to disregard the 14.57 in the a/f table. Tuneecu lets you look at and change values in the fuel, ignition, a/f tables etc. It doesn't tell you the actual a/f ratio. Your wide band sensor does. Can you continue to get readings from that with the Dobek disabled?
Could you say again what exhaust you have?