I think this question might be best answered by a professional sofer or someone who has written a Torah even once.
There is a fairly "strong" minhag to place the verse of Ma Tovu at the top of the column. Actually, there are 6 verses that start at the top of the column, though the 1st one, is the first verse of the Torah, so that's easy to do. I learned last week that a Torah need not be written in sequential order.
I'm curious what sofrim do to assure that verses like these happen this way. Do they begin writing each of the 6 verses first at the top of a column, perhaps at the start of a new piece of parchment, and then write the rest of the Torah to "fit in" to these verses? How do they accomplish this "feat"?