Ok an update to my Makerbot Desktop issue. I found that when I enter the Custom Settings and made a custom profile for my settings, sometimes it would cause the program to fail with an error message when previewing or printing. I think there must be some sort of combination of settings in my profile that Maker doesn't like. This is a bug because if two things can't be true or causes a processing error, it should give a warning message. If I use the standard profile or one of the default custom ones like (Standard) it works fine.

Another thing I learned is how to better control the extruders in the Maker software. There are many places to set it and you have to be aware of what each thing means. For example, if you want to print a part with the left extruder that has supports or rafts, and you want those supports to be in the same material (same extruder) you to choose Mixed Material Support. That's kind of strange right? I would think that if I checked that box, it would print the object with one extruder (say PLA) and the supports with the other extruder (ABS). But in this case, Mixed Material Support means "use the same material / extruder for the entire print"

Does anyone know how to adjust the print speed in Maker? There's a menu for extrusion speed but it's split up into Bridges, First Layer, First Raft Layer, etc. Which one is the "main" print speed for the rest of the object? Is it Infill?