A player can be a backup and or reserve at more than one position. A player can be the backup at one position and a starter at another.
So if your PG is A, with a backup of B;
and your SG is C, with a backup of A;
Then B might come in for A; and then A come in for C.
I'd probably be sure to have 2 players for each position, one the starter and one then the backup, and then have your 11th and 12th players be a reserve for a couple of positions, and the other starters and backups be the reserve for the other 3 (your backup C, might be the reserve PF, for example).
It is pretty normal for the 11th and 12th players not to play at all, or perhaps just get a couple of minutes of play. It might be a little different if there is an injury or players foul out.