What to expect

run CrossStitch.exe.
You will see the following three windows:

Main  Window
Thread  Window
Results  Window

The first thing you must do, is select a bitmap file to use.  Bitmap files have the extension ".bmp".  From the File menu select "Create a pattern from a .bmp file"

You will see the "Open File" dialog box.
Select a file and click "Open".
The three windows which first appeared will now look something like:
Main  Window
Thread  Window
Results  Window

Let's explain the controls on the main window.

This is the name of the file you chose.

Specifies how many pixels from the source image should be combined into one stitch in the results window.

Specifies how big each stitch in the results window should be drawn.

Specifies how many blanks to display between each stitch in the results window.

Specifies the background color to use in the results window.  0 = Black, 15 = White.

Lets you bias the color of the results window.  You may individually tweek Red, Green and Blue.

Only use threads from thread.ini which have a priority greater or equal this value.

Specifies how many times a thread must be used to not be considered "Rare".

Only display stitches made from threads which are selected in the thread window.

You can't hurt anything by trying each of these controls and observing what they do.

Marking your progress

In this example:
I've clicked "Only Show Selected Threads"
I've clicked "1058 Medium Cornflower Blue" in the thread list.
I've Right-Clicked on the bottom-left 29 squares.
The title bar tells us that I've selected 29 of the 1508 squares or 2%.
You may Right-Click and drag to select several squares.
Use Control+Right-Click to deselect a square.