There isn't any manual that I know of. The line of squares with numbers is the game's save icon. Whenever you see it, it means the game has just saved. The numbers change, but it's merely cosmetic.

For the white icons with black designs, can you elaborate more? I'm not sure if I saw those when I was playing.

Thanks for the reply.
Examples of these icons are:
black upside down arrow with ellipse at the point on white square
white exclamation mark on black background on white square

The exclamation mark means your objectives have been updated. Press 'M' when you see that icon and then left click and Artyom will bring up his current objectives that you must complete to further the story.

The black upside down arrow is when your map is updated. When you visit a point of interest, that will update the icon on your map from a '?' to whatever type of place the location is. You can access the map by pressing 'M'.

I would've liked a manual for the game as well; it seems a lot of UI stuff and mechanics you have to piece together from just playing a while. But it does add to the immersion though, and make me feel like I'm growing like Artyom.