Please use the load remover if you are on PC. However, if you did not use it or are on console, you can record your run without it then manually subtract load times. Loads happen any time you fast travel or reload autosave. Subtract the time starting when the screen turns black until you have character control. Also, there is one at the end of the intro when you reach the boat. Subtract the time that the loading icon is visible in the lower right corner. You can watch the PC runs with a load remover to use as a reference for when the load remover starts and stops.

I just use notepad to make a list of the load times every time a loading event takes place. Then add it up and remove that from the real time. Then you will enter the actual real time and the in game time (time without loads) when you submit your run.