If it were me, I'd wait until it got a bit taller before pinching and topping off the soil mix. Also, I'd pinch the first blossoms so the plant can direct it's energy to growth and root development.

If it were me, I'd wait until it got a bit taller before pinching and topping off the soil mix. Also, I'd pinch the first blossoms so the plant can direct it's energy to growth and root development.

You can 'bury' tomato plant anytime, it will not hurt it. It will grow lots of roots from the burried part of stem (better for the plant).
You can wait as 41n suggested, then cut off bottom set of leaves & top with more soil, or you can do it now. You could also pinch off the flowers now as suggested.
(BTW, is there a good drainage?)
Rina