If you have a small screen, or just like to keep it neat, there are a number of things you can do to keep your folding status information tidy.
Compact Windows
If you click the "zoom" button (small green sphere, top left corner) of a document status window, you will toggle between "normal" and "compact" modes. Compact mode shows only the status icon and the estimated time remaining. Here are the two views:
Align Windows
With the "Snap Windows" option enabled in the Window menu, your windows will automatically nudge themselves around so their edges stay lined up. To make small adjustments without this nudging, hold down the Option key while dragging a window.
Float Window
In the settings pane for a document, under the Display tab, are several settings related to a document window's appearance:
"Float" will cause this window to always be on top and visible, even if other applications are running.
Transparent Windows
By sliding the slider control in the Display pane (above) you can render a document's status window partially transparent. This can make it less obtrusive, especially if it is set as Floating, while still keeping it visible.
Dock Icon
In the same Display pane is a checkbox indicating that this document would like to be one of those whose progress is shown in one of the two bar graphs in the dock icon. Zero, one, or two documents' progress may be displayed in the Dock icon. If this option is turned on for more than two, the first two in alphabetical order are used.