The main colour control allows you to specify exactly what colours things should be displayed in. To modify one of the PuTTY colours, use the list box to select which colour you want to modify. The RGB values for that colour will appear on the right-hand side of the list box. Now, if you press the ‘Modify’ button, you will be presented with a colour selector, in which you can choose a new colour to go in place of the old one. (You may also edit the RGB values directly in the edit boxes, if you wish; each value is an integer from 0 to 255.)
PuTTY allows you to set the cursor colour, the default foreground and background, and the precise shades of all the ANSI configurable colours (black, red, green, yellow, blue, magenta, cyan, and white). You can also modify the precise shades used for the bold versions of these colours; these are used to display bold text if you have selected ‘Bolded text is a different colour’, and can also be used if the server asks specifically to use them. (Note that ‘Default Bold Background’ is not the background colour used for bold text; it is only used if the server specifically asks for a bold background.)