First, the map template for a map 'square':
It is 256 x 256 pixels in size, because each room is always a multiple of 256 pixels in width, and because there's always a multiple of 256 pixels in distance between the tops of different rooms. The top line is where a room will begin, the middle one is where it will end, provided a room does end in that square, and the bottom line is where you'd put another template right under it for the room below.
Now, for some examples:
Example 1 - Single screen room (256 x 207), no scrolling:
This one is simple. The room is of course aligned horizontally, and vertically it is aligned on top of the square (including covering the top red line) and it ends right on top of the middle red line. The zone left under (including the bottom line) is exactly 49 pixels as I already said.
Example 2 - Single screen room in width, with vertical scrolling:
Now, again the room is aligned horizontally with the borders of the template and again it starts on top of the top red line. However, since the room is actually two 'squares' high, I put another template right under it. Just like in Example 1, the bottom of the room ends just over the middle red line of the second template.
Example 3 - Room with multiple scrolling:
This is actually just like Example 2, except that since the room also has horizontal scrolling, I simply put another series of two templates right next to the first. No real explainations needed here.
As you can see, the bottom of a room will always be 49 pixels short of the bottom of a template. That's why I said that to get the total height of the map, you had to substract that 49 pixels since that's where the map will end.
Also, once you'll start mapping the Inverted Castle, simply flip the template vertically as well as the alignment rules. Align rooms at the bottom of templates and the 49 pixels gap will be on top instead.
Revned and everyone else, feel free to demand more precisions to make sure you understand well.
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"With the first link, the chain is forged. The first speech censored, the first thought forbidden, the first freedom denied, chains us all irrevocably." [...] The first time any man's freedom is trodden on, we're all damaged. - Captain Jean-Luc Picard
B*tch, meet reality. Reality, meet b*tch. - Me