I'm assuming the method 1 you are referring to is this:

and method 2 you are referring to is this:

which for those who don't know can be added to your toolbar using File > Global Preferences like this:

. If you know the time you want to stop in day:hour:minute format, then method 1 is quicker and more direct. By the way, you can use decimal minutes in this format if you want, so 03:09:31.56 is allowable and means day 3, 9th hour, and 31.56 minutes.
If you want to stop at a particular time reported by the System Console in minutes, then method 2 is the way to go because you can copy the time from the System Console directly into the Set Stop Time window and when you hit OK, it will convert it into dd:hh:mm format and fill out the "Clock time for end of simulation" field for you automatically. The two windows are tied together!
I like to copy all but the last couple of decimal places from the reported error time, paste it into the Set Stop Time window, hit OK, reset and run the model at Max speed up to the new stop time, then open the Debug > Event List window and look for the scheduled event that matches the reported error time exactly. It should be the next event or two to happen in the list, so it will be up at the top of the Event List window. Hopefully, there is some useful information associated with the troubling event that I can use to figure out the problem, or at least the object/patient in the model that the event will occur on.