So should I just stick with the red highlight of 250 on the speed dial or is there a way to calculate manually?
Calculating electronic flash exposure manually has nothing to do with the shutter time, unless you include ambient light. Then you have to meter/calculate the ambient light exposure at the set shutter time and aperture. Depending on how far (in exposure stops) artificial and ambient light differ, you might want Change one them.
With a flash in manual mode you might be able to set it at lower power, vary its zoom-head, use indirect lighting. The ambient lighting then is typically controlled by the shutter time as this only would effect the ambient part.
BUT:
Some basic cameras set a certain shutter time the moment any flash is pushed into the hot-shoe.
System SLRs with dedicated flashes typically set their synchro shutter time the moment that dedicated flash is installed. I assume that is so in your case.
I guess some expert on your Nikon combo will chime in to give details.