How can u just upgrade a player in attack or defence only when he has a low control ball skill or a low passing or low speed and mentality?i dont get that part of the guide...

Not sure what you/he want to say but I think you can click on skill point and then add him where you want defence or attack depend on player possition.

IS it really better to have the same formation in all the season or change it depending your enemies formation?cuz i ve seen some really good managers here changing plans every game.

If you are using only 1 formatiin at the end of season normaly your team should be stronger as long you will play with same 11,