I believe there are two ways.
1. You push a button at the playcall screen to switch through different packages as you normaly would
2. This is the method I like a lot.. is that abov ethe playcall screen you have a picture of your formation... you can go that box and then navigate to whatever player you want to sub out, click on the player, and then pick his replacement. It works great, unfortuatnely you can only navigate using left and right, so if I'm on the QB and just want to replace the HB instead of pushing DOWN I have to hit left or right until I get to him... which is the main reason for my post.