After the PCB is fully layed out, then you do a refdes renumber starting at the top left of the board, and proceeding to the lower right. I believe the renumbering is based only on component position, not on any functional grouping. Then you backanno the new numbers to the schematic. Done right (I don't know the algorithm), this tends to place components with close refdes numbers near each other.
In Protel there is the choice of doing it horizontialy (H) or Verticlly (V). H: Starts at the top left of the board and goes as a strip to the right side then wraps back to the left side for the next strip. This seems to be the most common. V: Goes from Top Left down the left edge, then back to the top in colums. Depending on how many parts you have and the size of the board C100 could still be next to C200 in the column setup. C200 could be under C100 in the strip setup. The strip layout helps out the people stuffing the boards and helps the technichins in the repair department, while perplexing the enginner that did the original schematic for a while.
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