You're not going to get very far in the game if you don't know how to use the controls! The directional pad obviously moves your farmer around and navigates up and down through the menus. The rest of the DS' buttons are assigned to other tasks.
The "pick up" button. You only have to stand facing an item on the ground and then press the A to pick it up. If you press A again then you will throw it back on to the ground. You also harvest your crops with this button, and start conversations with the villagers. You can even talk to your animals!
Hold down the B button and press the directional controls to make your farmer run. You can do the same thing to make your horse run faster.
When you are holding something edible in your hands, you can eat it by pressing X.
What you have in the red-colored Tool slot in your rucksack will be used when you press the Y button. Hold down Y if your tool has more than 1 level and you want to power it up. You can also plant crops if you have a bag of seed in the red slot of your rucksack. If you were holding something (via the A button), pressing Y will put that item into your rucksack.
This will pause your game where ever you are. Unfortunately when you pause the game you don't have the ability to interact with your lower screen. There's no way to pause your game to stop time, access items in your rucksack, and then unpause to continue.
It is not used and has no purpose.
Left Shoulder Button
To whistle for your pets you just have to press this button. Sometimes the pets will come to your call, but most of the time they'll just ignore you like pets typically do. You can also whistle at the villagers when you see them, which will cause them to pause for a moment.
Right Shoulder Button
The Right button on it's own doesn't do anything at all. If you combine this button with one of the face buttons you can rotate between the different equipped items in your rucksack. It will typically be easier for you to use the touch pad and the stylus to do these same tasks, especially if your rucksack has a lot of junk stored in it.
Right + A Button
The items that can be held above your head will be switched. As you hold Right and press A your character will hold a item above his head, then switch it with a new item from his rucksack. This rotates the content of the rucksack's Green slot.
Right + B Button
This will rotate the equipable tools from the rucksack's Red slot.
Right + X Button
Rotating your different accessories into your rucksack's blue Ornament slot is done with this button combination.
Right + Y Button
This will do the same tool rotation as the Right + B Button command, but this will reverse the rotation of the tools. If you had rotated past the tool you wanted with R+B, you can reverse it with R+Y to get the tool to reappear in your red equipment slot.