Welcome jchcambers 1978.
To just add to and ditto what gravehearted has already said. The reason that they may now seem to have unlearned their litterbox habits is that they may be reaching sexual maturity, (usually around 12 weeks) and now their hormones are driving them to mark. Becareful to watch that they don't fight, and if they are opposite sex that they don't mate.
Having them spayed/neutered will really help them get back on track. It can take a month or longer for their hormones to die down though, so for now it sounds liek you will need to limit their freedom for the time being so that they can establish "THEIR" territory and know it differs from yours or the general territory. Do you have pen so that you can limit their freeddom, yet give them enough room to exercise?
It's a good idea to to do this asap, as bad habits can set in even if they are just hormonally driven right now.
I also agree that you should get them sexed asap because you don't want to separate them if they are not fighting as that could make them unbond, but then the other scenerio of one getting pregnant (expecially at this young age) is worse. If you still can't figure out which one is which, then maybe a rabbit savvy vet or nearby rabbit rescue would be able to help you out.
At this time, testicles should drop, but males can pull them back up, so you can't always tell that way either.
Keep us updated.