Yep - you'll get the CPU with no subbing, but you can use the rotation you want on both O and D.
Put your 3rd down back in the #1 and #2 spots as someone different as well. That, combined with package subs can get 3 backs into the rotation.
For example, my HB:
1) Caulder, 2) Grant, 3) Jones
I package sub Grant in.
3rd HB:
1) Grant, 2) Jones
When it's 3rd down and I pick a formation with Grant in, it goes to Jones. I can run with Jones (no fumble, no fumble, and....stop!), getting 3 guys in with carries. And if you trust your FB as well, you can get four guys in. I usually don't because Grant and Caulder is usually good enough running and Jones I'll throw to and Reece I'll throw to, but it gets them involved and maybe some XP. Like if Jones has the 1 TD catch goal - if I can get that in on a 3rd down, it's some XP for him, even if he does nothing else.
Defense subs are harder since you have to know who comes in. I'm still learning it myself (I want my formation subs!!!!!
) One I like is using 3-3-5 Normal LB Rush. That will bring down your starting OLBs to the DE slots and then your #2 OLBs come in. I put Kindle and Worilds there - two pass rusher LBs and call blitzes out of the 3-3-5 with Worilds as the LOLB since he's better (relatively) in coverage (LOLB seems to blitz less often from that set). You could go with 2 Tampa 2 LBs in there and boost your second level coverage if you wanted. I did this with Nickle Normal in the 4-3 playbook too since my ROLB has no business in coverage - but he's a decent pass rusher. This puts his hand in the dirt and my backup can be a cover LB and can come in.