How do you do multiple backups?

Is it possible to have multiple switches at backup? Example. Prado is in lf Morales at 1b trout in cf. Morales gets injured.
can you make Prado move to 1b, trout move to lf, and have bourjos come in to play cf?

Good question. I wish I had a definitive answer. Sometimes you can set it up where the computer will make switches similar to what you want. Use your "Defensive Replacement" selections and your backups on the lineups page. I think the computer manager does a decent job, and it seems to have been improved over years past.

From the SOM Wiki page:

The last paragraph tells you about a problem they know of that will prevent a manager making the moves he wants, especially when you have 1 backup for multiple positions that requires a current starter moving to another position in the field. Since they know about it, i wish they could fix it.

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Sample depth chart
2B: Chase Utley (backup: Freddy Sanchez)
SS: Freddy Sanchez (backup: Bill Hall)

At the start of a game, if Utley were unavailable to play, the computer manager would try to insert his first backup, Sanchez, into the starting lineup at 2B. Since Sanchez is normally the starting SS, the computer would play his backup, Hall, at SS, so that Sanchez can slide over to play 2B.

At present, although the system is able to perform multiple, separate shifts in the same lineup, it can only handle one level of a given shift. In other words, using the above example, if Hall happened to also be in the starting lineup already (e.g. in CF), instead of moving Hall to SS, it would pull someone from the bench to replace Sanchez.

First, in-game injuries will be handled however the SOM engine wants, nothing you can do about that.

Second, depth chart is that. Goes in order, so it won't move someone from first spot to a 2nd spot, unless there is no other option.

With injuries the backups listed in your lineups are irrelevant. Hal only uses those to determine the game starting lineup.
For injuries not even the great Wizard of Oz could tell for sure what logic Hal uses. I imagine given the unlimited possibilities of rosters that might exist programming that is a bit of a nightmare. Probably need to cut the programmer some slack on this one.