(1) I'm not sure what you need to do, but you can save a model to an .sbproj file via the desktop or the command line and then load it inside an .m file as follows:
project = sbioloadproject('filename.sbproj');
model = project.m1;
(2) After you follow the above steps, you can simulate the model in the .m file:
[time, species] = sbiosimulate(model);
(3) There's no easy way to pause the simulation between time steps, but you can do something similar by causing the simulation to end after a specified number of time steps. Here's how to stop after 20 time steps:
configset = model.getconfigset;
configset.MaximumNumberOfLogs = 20;
[time, species] = sbiosimulate(model);
