It often helps to use other, similarly sized pieces to provide easier snap points from another direction. For your problem example, try snapping a vertical beam to the end of the wall, another on top of that, then the second layer wall onto that beam.

Wooden pieces are effectively one or two dimensional shapes as far as the build engine is concerned, but some have wider 3d meshes around that, which is the thing you're trying to aim your mouse at. The later stone pieces are fully 3d cuboids which can be a lot easier to work with (but tricky to embed into each other for curved walls) and core wood beams are confusing because the vertical ones are 1d lines like regular wood, but the horizontal beams are actually 2d panels, effectively 1/4 height walls.

Oh, also note that the small wooden door is, like stone, a full cuboid with 1/4 thickness and multiple snap points along its shortest edge. It's very useful as a guide for lining up other pieces. Four small doors face to face act as a ruler with snap points every 1/8 of a wall panel.