I just got the software last week and am loving it with my PrintrBot Simple Metal.
I have a part that I need to pause the print to insert a magnet and then resume the print so it can enclose the magnet in the print. Problem is my magnet won't fit unless the extruder is retracted. I tried manually doing this but it didn't work. I am using octoprint as my print server.
You can do this,you just need to know what layer you want to pause at. Using the G-Code previewer set to preview by layer, it gives a good visual representation of the layers and helps figure out what layer you'd like to pause at. After this save Toolpaths to disk, open the Gcode file with a text-editor and then add a new line with "M0" (No quotes) after the layer you'd like to pause at. Now save the revised G-Code file. Then go back to Simplify3D, open the Machine Control Panel and click the Print button which will open a file browser and you can use that to browse to the revised G-Code file. When the M0 is read, the software will pause and you can use the Jogging functions to retract/extrude/move around/change filaments. You can decide when you will restart the print by hitting the resume button.
My advice is to home the printer though in the X and Y-axis if you move the extruder at all, otherwise there will be a shift in your print.