When you edit a file in the queue, it gets saved in the same directory the original file was in. If your original file was an STL, the edited version will get saved as an AMF instead. If your file was already an AMF, it simply gets overwritten.
Unfortunately, right now MatterControl suppresses any errors encountered when saving files. If, for instance, you do not have permission to write to that directory, or there is no space left on the drive, then MatterControl will continue as if nothing went wrong and won't inform you of the issue. This is something we are investigating and will hopefully have fixed in the next version.
Assuming you're referring to something like Slic3r's XY Size Compensation feature, MatterControl does not have a built-in feature that will perform the same function. You'll need to either edit the steps per mm in your printer's firmware or EEProm Settings, or manually change the model's size to compensate for the inaccuracy.
> I don't get a very nice surface anywhere I have support. What settings do I need to be looking at?
The ones I mentioned in my previous reply are a good place to start. The interface layer tends to create problems, so I typically just leave that out. The X, Y, and Z distances create a gap between the model and the support which can affect aesthetics, so adjust those as needed. Just don't make them too big, or the model's overhang will droop.
What's changed from when you were able to print and when you weren't? There's got to be some variable that will explain it.
Try printing a different, smaller model with the same settings. If it prints, it's just the model. If you have the same issue with the smaller model, then there's one or more settings causing the problem.
You say it is able to extrude manually using the controls. That narrows it down a bit. It means its not an electrical or mechanical issue.
First thing you should do is check the gcode terminal while printing to see if any errors are being reported by the printer. For example <-echo: cold extrusion prevented. If nothing shows up in there, then lets make sure that MatterControl is actually telling your printer to extrude. Export both the gcode file and your slice settings and post them.