I have always manually assigned the skill points, though some people like to use the auto, I feel you are better off choosing which areas you want to strengthen.

You have the right idea, if you have a guy at 9 he will be more attractive on the market! When is up to you really, but of course the first few days of the Season it is a Sellers' market! I myself sell (and buy) towards the end of the Season, and those who don't sell go on the first day of the new Season. But it is really a bidding war for anyone at begin of Season, so to buy players then can be really hard.

I can't comment on Scouts... I don't buy them.