I managed this for a long time. If you keep the fatigue as 50, I would recommend you to put 99 sub out and 100 sub in for HB. That way your backup HB will get something like 5-6 carries per game... What I do is put the fatigue in 80 and put 98/99 out/in.
About the QB 49/51 in a 50 fatigue means that the backup QB will never see the field (unless the startig QB gets injured).
In my league I use 80 fatigue and the following auto subs:
QB - I don't care, because I don't want to share the work with the backup...
HB - 98/99 (Backup gets 8-12 carries per game)
WR - 97/99 (Even the 6th receiver has few snaps - something like: let's suppose 60 snaps in the game: 1st receiver: 45; 2nd receiver: 40; 3rd receiver: 30; 4th receiver: 20; 5th receiver: 10; 6th receiver: 5.
TE/FB - 96/99: Your backup TE will be the starting TE for something like 15 snaps. If you have a backup FB and/or 3rd TE, he will get a few snaps as well.
OL - 95/99: Backup OLs will get something like 12-13 snaps.
DE - 96/99: Backup DEs will get wsomething like 14-15 snaps.
DT - 95/99: Backup DTs will get something like 12-13 snaps.
LB - 96/99: Backup LBs will get somethig like 14-15 snaps.
CB - 90/99: 1st and 2nd CB will play almost every down, 3rd CB: 35; 4th: 15; 5th: 5.
S - 90/99: Starting S will play almost every down, backups will get 10 snaps or less...
That way all my backups play a little bit...
I hope I helped you... Any doubt, ask me!