In order to play TPF Fallout 4, you must launch f4se_loader.exe through Mod Organizer 2. Otherwise your mods will not work. When you open Mod Organizer 2, F4SE (renamed to Welcome to Paradise for your convenience) should be selected automatically in the executables drop-down and you can start the game by clicking Run.
Shortly after the character creation, you will get a prompt which is added by the mod Start Me Up. You will be asked whether you want to “relive the memory”, giving you the option to skip the prologue. Do not select this option if you never played Fallout 4 before, you are going to miss some important things.
If you want to play the regular Fallout 4 intro (highly recommended), click “This is a memory. Let’s stay here a while” and the prologue will play out as usual. Proceed to the Mod Configuration page after exiting the vault.
Intro spoilers ahead.
If you do choose to skip the prologue because you have played it a hundred times already, select the second option: “This is a memory. I don’t want to relive this.". After a fade-to-black, you will find yourself waking up inside the cryo pod shortly after a certain someone shot your spouse. Note that the door to the hall is locked until you interact with the terminal (left of the door), configure your SPECIAL stats and enter a name.
Play through the intro as usual and continue with the Mod Configuration section after exiting the vault.