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Post #24 Shaefer’s Season 2 Let's Play Silent Hunter 5 YouTube Videos 
The squares you refer to is the Kriegsmarine Grid Map.
I will try to explain how it works as best that I can.
When you request a mission you will receive a grid reference to patrol.
This will not happen on the 1st Mission (Baltic)
This appears in the Captain's Log i.e AN5544.
The first reference i.e AN55 you will see on the navigation map.
The last 2 numbers i.e. 44 breaks down the grid reference into smaller sections.
Use your mouse wheel on the navigation map to enlarge AN55
Press the E key and scroll in the top section to find Maps and tick the box.
Scroll in the lower section and tick the Light Grid box.
Drag the Grid on top of AN55 and drag the side and the top to fit the grid.
In this instance we are looking for 44.
You will see the section 40
To complete the grid reference you need the number 4.
I use my ruler tool and marker to draw the area
Each one of these small rectangles I measure out to approximately 20km x 10km
Grid AN5544 showing in AN55
Enlarge the map to remove the Kriegsmarine Grids.
You will receive your patrol orders in a radio message.
You can use the compass to draw out the 80km from the center of AN5544
This may also show in the Captain's Log radio messages as in picture 1.
You must not make a manual save when entering the area.
The 48 hours game time has to be completed in 1 session, or pause the game and hibernate your PC.
You will be told when this has completed.
It is useful to use the ! Player Objective Icon which can be minimized when it appears at the top of the map.
This will turn from yellow to green.
Each completed patrol area is worth 1 bonus point.
This is the way I do it, there may be better ways, but I am sure seeing this you will find your own way.
Peter