Hi Chaser,
Considering your puppy is only 3 mos old, this is what I would do:
The very first thing you want to teach your dog is to pay attention to you. Call her name and if she looks at you tell her "Yes!" right away and give her a treat. I don't even hold a treat in my hand. I always wear a treat pouch (in fact, I use a small shoulder bag made with old jeans) so that the dogs cannot see treats. I can even shift the bag to my back

.
However, when I teach "Sit", I hold a treat with my fingers and bring it close to the dog's nose and move it over his nose so that he would automatically put his bottom on the ground. As soon as his bottom touches the ground, I say "Yes!" and release the treat. Repeat this several times before you introduce a verbal command of "Sit" along with the hand motion. When he masters "Sit", I will no longer hold a treat with my fingers but just a hand motion (that looks like I am still holding a treat in my hand). At this time, I still say "Yes!" as soon as he sits but a treat will come a second later from my pouch. This way, he will just follow the command with my verbal command and my hand motion but he will know that a treat will come later.
Teaching "Down" is the same thing. First have him sit and and bring a treat down in between his front paws so that his nose will follow the treat and bring his body to the down position. After a dozen times, I will introduce the verbal "Down" along with my hand motion as if I am bringing the treat down but without a treat. Always "Yes!" right away, followed by a treat.
Instead of "Yes!" you can use a clicker. Dogs will know that he did the right thing with those markers (Yes or clicker sound) and that a treat will come soon.
Hope this will help