This can take some testing to know what will work best for your organization's area and pets!
Checking "special needs" will mean that the pet will also show up in searches for special needs pets, and will not affect them appearing in normal searches too.
Since the checkbox can be easily checked and unchecked and the change will appear instantly as soon as you click the update this pet button, you can give both ways a try to see what helps your pets connect with potential adopters that are interested in adopting them.