I don't use Blender but the basic way I go about modelling level architecture is this:
1. Set up a 16 x 16 or 32 x 32 grid.
2. Turn on a precise snap to grid
3. Create the basic architecture (walls, floors, halls, etc using planes and polygon box modelling
4. Keep it separated up in a logical way with an idea of the texture maps in mind
As long as all your architecture pieces are snapped to the grid all should be fine.
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