Any changes made by hidden layers will not be seen in the saved image. What you see in the viewport is what you'll get in the saved image. If you want the changes made by hidden layers to be seen in the saved image, you must first go to the layers list and unhide the layers before saving.

If you would like to simply save the file in the existing format and with the current file name, you may click the Save button on the toolbar, or choose the Save option from the file menu.

If you would like to save the file in a different format or with a different file name, click the Save As button on the toolbar, or choose the Save As option from the file menu.
If you would like to save your photopad project with all of its associated layers, choose PhotoPad Project from the Save as type dropdown menu.

If you would like more options, select Save for Web from the File menu. This will open up a dialog which will display a preview of the image you are saving (in the left pane) as well as a preview of what the image will look like in the chosen format (in the right pane). If the image is larger than can be displayed in these panes, it will be resized, and you can move your mouse around the images to display a small box that shows you a 100% crop of the area the mouse is over. Once you are satisfied with the resulting image click OK and a dialog will appear allowing you to name the file and choose its destination.
File Options
The pulldown list allows you to select the file format that you wish to save the image in (JPEG, BMP, TIFF, GIF or PNG). Changing the selection will cause the preview image to update (right pane), and will also update the Projected File Size. The Projected File Size is the size of the image if you were to save it with the current options.
Format Options
Depending on which format you choose, there may be options available to control the quality of the resulting file (as well as the size of that file).

• JPEG
  There is a slider that lets you select the quality (lower numbers give a lower quality image and smaller file, while higher numbers give a better image at the expense of a larger file).
  
  
• GIF
  There are two options available for GIF files, Fast GIF Conversion and Use Dithering. Fast GIF Conversion is selected by default, and automatically uses dithering in the resulting image. This usually results in the smallest GIF possible, though it is not possible to save transparency with this option. Unchecking Fast GIF Conversion will result in a slightly larger file that takes much longer to generate, however it will be able to save transparency data, and usually will produce a better looking image. If Fast GIF Conversion is unchecked, you may select Use Dithering, which will attempt to blend the colors together to reduce the banding effects that can occur in gradual gradients.
  
  
• BMP
  This format does not have any options available.
  
  
• PNG and TIFF
  These 2 formats do not have any options available.