Navigating through the game is fairly simple. The START and SELECT buttons on your Nintendo 3DS are not used in the game. If you own a NEW Nintendo 3DS (N3DS), the special C Stick is not used either.
|Circle Pad||Move your character|
Highlite a menu option
|Directional Pad||Change the highlited square when working a field|
Highlite a menu option
|A Button||Confirm menu selections|
Talk to a villager
Do an action
Close an opened menu
|X Button||Open the main menu|
Trash an item when viewing your bag
View details when accepting a request
|Y Button||Open the Cultivating Menu|
|Left Button||Move the camera view counter clockwise|
|Right Button||Move the camera view clockwise|
|Left + Right||Move the camera view directly behind you|
The regular mode of your controls works like an auto-select action menu. When you stand next to a tree, the action prompt in the upper-right corner of your screen will give you the choice to "Cut Down" the tree. Standing next to tilled soil will prompt you to "Plant Seeds" when you press the A button. You can then press A again to "Water" your crops, press A to "Fertilize" the crops, and again press A to "Harvest" your mature crops.
Basically, the game will use the appropriate tool or item when you need it and if you have it in your bag. Standing next to water will prompt you to use your fishing pole, standing next to a rock will prompt you to smash the rock, and so on. You won't need to search through your bag to equip the appropriate tool, as the game will do it for you.
On the other hand, sometimes the menu can equip and prompt for tool use when you don't want to use them. For example, if you planted crops directly next to a water path, you move your watering action too close to the edge of the field area, and the prompt for Fishing appears as your A-Button action. Then when you go to water your next field space, you pull out your fishing pole instead. The best way to avoid this is to keep an eye on your prompt and make use of the Directional Pad to select the crop field to be watered. There isn't a way to store your tools inside your farm house to prevent the unwanted prompts from triggering.
The other menu you have access to is the Cultivating Menu. You can access these commands by pressing the Y Button. This menu allows you to sculpt the land of the valley. You can dig the soil by pressing the B Button while in cultivating mode, and build up land by pressing the X Button. For planting crops, use the A Button to till the soil. If you are in Winter season, then you first have to shovel the snow off the ground before you can till. Press Y again to close the Cultivating Menu.
If you are standing on stone ground, the B Button will change to an excavate command. You'll need to have a hammer to excavate stone, which is given to you as part of the Fall season storyline of the game. The stone you collect can be converted into Material Stone by asking Brutus to refine it. You can't use the stone to build up land though.