In the upper left-corner of your screen you'll find your current Hit Points and Rune Meter, which shows how much Rune Points you have. The HP and RP system is similar to the Strength and Fatigue system in the GBA and DS versions of Harvest Moon, but a little different at the same time.
The tools, weapons, and spells you use will vary in how much RP is expended. The watering can uses less than 1 RP per use, while the high level Earthquake spell uses up 16 RP in one cast! On average your weapons will use 2 RP per swing.
Each morning when you awake you'll RP will be at 100, and they'll decrease as you work on your farm and fight in the caves. You can recharge your RP by going back to bed for the day or by growing crops. When your crops mature they'll generate a Rune, which you can walk over to regenerate your Rune Points by 25. Once you harvest a crop from the 3x3 square of crops then the Rune won't appear. You also won't receive a Rune if only half of the crops mature.
Recharging your Rune Points can be done while you're exploring. You can bring food with you, but you'll find that most cooked items won't recharge enough to be very useful. The best RP recharging potions you can make aren't available until you've reached at least level 50 skill in alchemy.
Instead you can make your own Rune Factories from the crops you can grow inside of the caves. In each dungeon you'll find areas where you can plant seasonal crops. It's a good idea to plan ahead and plant your crops about half way through the dungeon. If you're not sure where the half way point is, you can check out the cave maps on the site. Don't forget to water the crops every day!
Once the crops mature and generate the Runes, you can easily use them as a recharging point as your trying to destroy all of the machines in the cave. Just destroy as many machines as you have Rune Points for, pick up the Runes from your mature crops, and then make your way to the end boss with a fully recharged RP bar.
One of the best things about making little Rune Factories from your crops is that the Runes will regenerate every day as long as you don't harvest the crops. A good place to make a set of factories is at the entrance of Toros cave, right next to your own farm. If you plant Fall season crops there and allow them to mature, you can use them to recharge your RP as you're passing back and forth from your farm to other areas in Andonea. You also don't have to water the crops once they've matured and begin to make Runes.