Your logo should be entirely within the blue box of the letter template, with no overlap of the red box, in order to print appropriately. Here's a link to our letter template. The space that’s viewable through the window is about .62 inches from the left edge of the paper and .5 inches from the top; in full it is about 3.26 inches wide and .34 inches tall. You can view our help center here to learn more about the letter dimensions.
If you're looking to print a color logo then ensure you're setting the color parameter to 'true' if you would like to print in color otherwise you can set it to false.