what level of stamina would you want to run with guys at each stamina level 

Would you run a guy with 99 stamina on tired? if so what outcome would you expect?

trying to figure out basically where stamina comes into play on performance.. like if a guy has 99 stamina and it takes him alot longer to get to tired. then setting it on tired could be a advantage at some point

what if the guy has a 50 stamina back up .. and is 25% worse as a player than the starter.. what would you choose

I have had problems with very high stamina starters. If I have made minutes promises to backups, they usually struggle to meet the goal.

I never go lower than Getting Tired because at Tired I have had guys sucking oxygen and take much longer to recover. Also, I never worry what my backups are set at because as soon as the starter is ready, he will go back in regardless of the condition of the backup. I set backups at FF and don't worry about them getting tired.

My impression (others can tell me if I'm right or not) has always been stamina indicates how long it takes a player's level of fatigue to increase.

So if you had two players, one is 99 stamina and one is 70 stamina, the first one will still be fresh at the point the second one is only fairly fresh or getting tired (depending on other factors).

It doesn't mean the 99 guy will perform any better when he does eventually become fairly fresh or getting tired or whatever, but it DOES mean he'll take longer to get to those lower levels (and perhaps recover faster too).

By the way, with most of my teams I set everyone to fairly fresh unless I have a reason not to do so because I want them all performing at their maximum (and usually starters end up getting more minutes anyway so it works out). Unless you have a star player who will still be better when tired than a backup would be at maximum, there isn't any reason to play them tired in my opinion.