Downstairs then Upstairs is the method I use when on the line, and ask my assistants to adopt when I'm in the middle.
The ball goes out of play and I make the mental decision which way I'm awarding the throw, at that point I either move the flag slightly away from my body to the left (for defensive, assuming left backs / right wings) and make eye contact with the referee to ensure agreement before bringing my arm up. For attacking, I swap the flag low down in front of my body, same eye contact to check the referee is in agreement and then up in the right hand for the signal.
If there has been a nick or blind side touch (from the referee's view), particularly in the middle or far third of the pitch, whilst the flag is low but away from my body I'll agitate it slightly so the ref can see I'm suggesting there is a non-obvious direction but I've got the best view so we can go together.
Rare occurrence is your view is blocked, you know the ball's gone out but have no idea who played it last - if the ball is now dead (rather than a fraction out and play continuing, flag held in front of me both hands so the referee can see I haven't got a clue so they can take control (that's why they get an extra £5/ game!), if a very close "in / out" call arises and play continues, same concept is in play but I put flag straight up and a cast a pleading look to the referee to offer a direction.
If neither of you can call it and player reaction doesn't 100% give you all the info you need - it's defensive all the way! If you cross, drop the flag and wait for the referee to either over rule you or to change his mind and acknowledge that you've made the right call.
Not sure of the statistics, but I'm pretty sure that throw ins will be the most frequent decision that needs to be made during a game, so the key is to make sure you are comfortable with either the instructions you are giving to your assistants, or are receiving from the referee, as whilst often inconsequential in the context of the game, getting throw in's wrong or crossing signals is a really easy way to lose credibility and look unprofessional.