Welcome aboard Vodo77!
We're always happy to get new members to harrass, er, I mean share our vast wealth of knowledge.
First, your save question. Those guidelines were for older computers where there were problems with the saves. I didn't have any problems if I didn't follow them precisely.
The most important thing you need to remember, is to save in a different file each time. Continuous save overwrites will cause files to become corrupted. I save while in port using my name, example "fireftr." While on patrol, I simply add a number, example "fireftr1, fireftr2," etc. This is independent of your computer hardware and is still true.
The patrol question. There is a lot on here about when to finish a patrol and how to go about doing one. It's really all up to you and how you want play. I don't refit, I use up torps then head back, or head back when fuel is getting low.
It is up to you when to go to the mods. I suggest when you're comfortable with the mechanics of the simulation, go ahead and mod. The mods really make it a great game.
Now join the crew polishing the propellers.