You don't have to lock her away in the actual jail with Tomy, just get her into the secret room by barking in it to summon dog food for her to eat. Once you've done that, run into the study and input the combination into the computer again to lock away the room so she can't come out.

To get the medicine for Tomy, you need to be able to get to the locked warehouse (the room with a lot of dog food stored).

So do it in this order:
1. Make sure you've fed CHRIS (the dog that lives in the dog house) 500 bugs in exchange for a DVD. Then put the DVD in the DVD PLAYER to see the number 3 pop out.
2. Get the STUDY ROOM KEY by going back to the dog house. You'll see that CHRIS is gone, but there are directions left for you to follow (up, then right). Go into the dog house and continue further up (there's a hidden tunnel, then turn right until you bump into Chris. Chris will then give you the STUDY ROOM KEY in exchange for keeping his tunnel a secret.
3. Go into the STUDY. Go to the computer and input this number sequence 4-7-6-3 (for the reason behind the sequence, visit this thread http://www.gamersunite.com/i-became-a-dog/themes/i-became-a-dog-computer-password ) It will then open a secret entrance into the JAIL.
4. Go into the secret room and speak with JULIA (the dog locked up there). She'll ask you to look for her PUPPY before she gives you the WAREHOUSE KEY.
5. Speak with CHRIS once more.
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Do I have to write everything down? I think it's pretty linear from there. Good luck~ and don't forget to support the game dev by giving a good review and watching ads.