The purpose of the initialization phase is to assign to each slot in the puzzle a list of all the possible words that may be used to fill it.
Ignoring for the moment any initial clues provided with the puzzle, the primary criterion for selecting words is their length. So the first step is to associate all three-letter words with each three-letter slot; all four-letter words with each four-letter slot; and so forth.
As for initial clues, there may be none—we may get only an empty framework. However, in general, the initial puzzle may show any number of cells filled in. The most common case is that one slot will have its entire word filled in, but the author has seen puzzles with more than one initial word placed, and also puzzles that had only a sprinkling of single letters here and there.
Conceptually, then, in the general case the initial clues can be represented as a set of cells that have their initial letters filled in. These initial clue cells can be used to eliminate some of the possibilities for one or both slots that pass through that cell.