I've built my NL team to run, but lately to get some pop I have signed some guys with pianos tied to their arses. My starting line up has 6 guys with over 90 and 2 guys with less than 50 speed. I have base running & stealing set to very aggressive. My question is does the AI apply that to every runner or does it consider the speed factor of each player. BTW, I have the hit and run at average because I really don't want the slow guys running, ever. 

It will apply the setting to all runners.  So the guys with less than 50 speed will be running more often than perhaps they should, but they won't be running as much as the faster guys.  And don't forget about the base running rating.  A guy with 95 speed and 12 base running is not going to provide the results you may expect from a guy that fast.