I would think the UI would work well being very similar to your current layout with the control functions on top and graph(s) for each pit stacked below.
It would be nice to be able to select the graphs tiled vertically, or to select a tabbed/page format.
Maybe you could split the control functions and graph displays into seperate windows so they could be scaled & moved around for best viewing and use of available screen.
There would need to be a check box, or some setting for each probe and blower to associate it with a graph (pit-1, pit-2, etc)
I think there is always a 1:1 ratio of blower to pit (and corresponding graph)
When I use more than one blower for a cook it is for a seperate smoker and has one pit probe associated for blower control. Adding a second pit probe is purely to monitor the temp at a different position or level within the smoker.
It is nice to do this sometimes to make sure the control probe is not being 'influenced' by a hot spot, or being to close to a cold chunk of meat. Also to learn the characteristics of the smoker at different grid levels.
For email (text to cell) short, concise, alarm notification would be great. (Alarm: Pit-1 High Temp 275, or Alarm: Left Butt Done 195)
Also a fixed interval (selectable) status update notification of current temps is handy.
(Status: Pit-1 225, Red Probe 169, Green Probe 172, Blue Probe 174)