I don't know for sure how it is calculated, but I assume it is based on the MET value and your weight. However, I rarely find the calories listed to be anywhere close to what I burn per my HRM.
Just curious if the read-outs are lower or higher on your HRM? I was surprised it told me I would only burn 450 in Interval Max, while p90x estimates one to burn 600 in Plyo X. I find IMax to be much harder!
I don't know what these are based on either, but mine are always lower on my HR monitor (when I use it) but sometimes not by much. With that said, I am probably smaller and lighter than whatever average they use so I'd expect the WO Manager to be higher for me.