.. How do I open the box with the circles and squares?

A glance at "Magnus's note" shows a description of this puzzle. Read to the end of this hint for a picture showing the solution.

The goal is to one of each design -- hollow circle, hollow and solid square, hollow and solid diamond, and solid circle -- in each row and column. You don't need to worry about the diagonals.

Pieces can cover other pieces only if they completely cover what's in that space. That is, a solid can cover a hollow, but a hollow can't cover a solid. A solid square can't cover a hollow diamond because it's too small, but a solid diamond can cover a hollow or solid square because it's bigger.

So it's ... a little like a geometric sudoku with more rules. Well ... a little bit.

The rule about what can cover what means that the biggest solid piece can only be covered by the biggest solid piece. So cover all the solid circles with solid circles.

If you have a solid square in a row or column that has a solid circle, it can't be anything other than a solid square. So you can place those too.

With that done, if a row or column has a solid square and a hollow square, the hollow square can't be anything but a hollow square.

This kind of elimination will get you started. After that, the usual sudoku strategies apply, to a degree.

Before long, you should be seeing rows or columns that have five out of the six spaces filled, at which point the final piece is obvious.

However, if you just don't do sudoku-type puzzles, here's the answer:

Secret Room Puzzle 2, Amateur

Secret Room Puzzle 2, Master

All this gives you a piece of Captain Lawrence's journal.

Where do I find all the journal sections?