I always put those old-timey runners with bad SB% on a 0 run setting, unless I notice my opponent has a catcher with a D- arm, in which case I'll switch it to 5. I recently had 1899 John McGraw -- RL 73/118 (62%) -- go 5-5 stealing in a game against a D- arm. Overall he's 14/18 in just over half a season, which I think is an acceptable rate.
I have an AAA OF in a 1996 prog who's 2009 Josh Anderson -- real life rate of 25/30 in 298 PA. I put him on a 5 setting for every catcher except the A+ arms (the setting is 0 then), and in 109 games he's 33/34. I did the same thing in this prog last season, with 1995 Tony Tarasco, turning a 24/27 real life rate into a 53/54 sim season. It takes a bit of micro-managing, but it's worth it.