I've been able to make this type of thing work with some juggling of my defensive hierarchies.  See for example the 9th inning of the game below where a replacement comes in for the LF and the guy who was in LF moves to 1B and the guy who was playing 1B goes to the bench.

http://www.whatifsports.com/slb/Boxscore.aspx?gid=19834526&pid=1&pbp=0&tf=10

Dunno if this will work but here is a paste of my defensive hierarchy

1B	'89 Harry Stovey	'90 Henry Larkin	--	--	--
2B	'70 Roberto Pena	'89 Lou Bierbauer	'29 Jim Cronin	'91 Curt Welch	'94 Lave Cross
3B	'94 Lave Cross	'70 Roberto Pena	'29 Jim Cronin	'91 Denny Lyons	--
SS	'70 Roberto Pena	'86 Frank Fennelly	'29 Jim Cronin	'94 Lave Cross	'91 Curt Welch
LF	'91 Curt Welch	'93 Eric Fox	'08 Herbie Moran	'89 Harry Stovey	'25 Bill Bagwell
CF	'91 Curt Welch	'93 Eric Fox	'08 Herbie Moran	'89 Harry Stovey	'25 Bill Bagwell
RF	'91 Curt Welch	'93 Eric Fox	'08 Herbie Moran	'89 Harry Stovey	'25 Bill Bagwell

With your first baseman Stovey listed fourth as an OF defensive sub it is not likely it will happen too often, but regardless of where he is in the OF defensive hierarchy, all you need to do is put the bench player as listed right after Stovey.

Or even before him - I admit I am a little unclear about whether regular starting players need to be listed first or not. 

So when Stovey goes to the OF the person you want should be the defensive sub at 1st base. You might want to click the function for "double switch" in the Manager's Center where you set the managerial style and put it on "Aggressive". 

Posted by italyprof on 4/8/2013 5:58:00 PM (view original):
With your first baseman Stovey listed fourth as an OF defensive sub it is not likely it will happen too often, but regardless of where he is in the OF defensive hierarchy, all you need to do is put the bench player as listed right after Stovey.

Or even before him - I admit I am a little unclear about whether regular starting players need to be listed first or not. 

So when Stovey goes to the OF the person you want should be the defensive sub at 1st base. You might want to click the function for "double switch" in the Manager's Center where you set the managerial style and put it on "Aggressive". 

Um you have it backwards. Larkin is the starting first baseman. When the time comes Stovey comes in from left to play 1B and Larkin goes to the bench. Meantime Herbie Moran comes in to play left and if ever a team need defensive replacements it is this one as they are on pace for about 375 (yep three seventy five) errors ... not a team that zubinsum would love for sure .....