You should set a cut-off date for quarantine, after which you do not add new animals to the same room as your quarantine room. Start your quarantine from the date that the last animal was added to the room.

There is a risk that one animal in your quarantine room will pass an illness to the other animals there, but at least your main collection will be safe, and you can treat the animals in quarantine. If you're not willing to take that risk, then quarantine the animals that come from different suppliers separately! Always treat quarantine bins/cages with Provent-A-Mite for 3 months, as mites can spread deadly diseases.

People will tell you to quarantine animals for 3 months/90 days.
This is completely inadequate. While many illnesses will reveal themselves within 90 days, some of the most dangerous viruses very well might not. There are nasty diseases out there which can incubate for up to 10 months.

Quarantine your animals for a full 12 months. The inconvenience is WELL worth the safety.