I use OneNote's SideNote feature to keep a note-taking window pinned on top of all other windows to do this sort of thing. EverNote (which is free in its basic version also might be a good solution).

I know there are a number of free or inexpensive window utilities (like Actual Window Manager) that can do this to any window (including a notepad or Word window). You might look into one of the freeware versions of this kind of utility to see if it solves the window focus and arrangement issue.

The beauty of OneNote or EverNote is that they create a source link for many kinds of information when you drag and drop into a notebook.